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Join the team (post here to be added to the bioconda team) #1

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johanneskoester opened this Issue Sep 13, 2015 · 794 comments

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johanneskoester commented Sep 13, 2015

Everybody is welcome to contribute a package. Simply reply to this issue and you will be added to the bioconda team.

Edit: After you post here, we will email you an invitation through github to join the bioconda team. Click the link in that invitation in order to be added.

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hyeshik Sep 14, 2015

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Johannes,
This is a great idea! I often felt the need of an OS-independent package catalogue for computational biology that works within the user space. After few minutes of trial with Conda, I could agree that it's a wonderful platform for such system. I would like to contribute packages that I use as one in the team. I have an experience as a package maintainer (so-called ports committer) in the FreeBSD operating system for ~5 years in the early 2000s.

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hyeshik commented Sep 14, 2015

Johannes,
This is a great idea! I often felt the need of an OS-independent package catalogue for computational biology that works within the user space. After few minutes of trial with Conda, I could agree that it's a wonderful platform for such system. I would like to contribute packages that I use as one in the team. I have an experience as a package maintainer (so-called ports committer) in the FreeBSD operating system for ~5 years in the early 2000s.

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johanneskoester Sep 14, 2015

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Great! I have send you an invitation.

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johanneskoester commented Sep 14, 2015

Great! I have send you an invitation.

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Hi Johannes -
I'd like like help with this, too. I like the idea of having one obvious place to find and contribute bio-related conda packages. I already have a handful of conda packages that could be useful here (https://conda.binstar.org/daler).

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daler commented Sep 14, 2015

Hi Johannes -
I'd like like help with this, too. I like the idea of having one obvious place to find and contribute bio-related conda packages. I already have a handful of conda packages that could be useful here (https://conda.binstar.org/daler).

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johanneskoester Sep 14, 2015

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Hi Ryan!
Great to hear that! I have sent you an invitation. Feel free to add your packages!

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johanneskoester commented Sep 14, 2015

Hi Ryan!
Great to hear that! I have sent you an invitation. Feel free to add your packages!

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johanneskoester Sep 14, 2015

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Btw Hyeshik, please also create an anaconda.org account so I can add you to the bioconda team over there, as well.

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johanneskoester commented Sep 14, 2015

Btw Hyeshik, please also create an anaconda.org account so I can add you to the bioconda team over there, as well.

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FYI, https://github.com/chapmanb/bcbio-conda has a lot of conda packages already. I'm not sure how much of that is tied specifically to versions needed in the bcbio-* packages though.

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daler commented Sep 14, 2015

FYI, https://github.com/chapmanb/bcbio-conda has a lot of conda packages already. I'm not sure how much of that is tied specifically to versions needed in the bcbio-* packages though.

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Good to know! Maybe we can invite Brad to migrate their stuff once we have reached a critical mass with Bioconda.

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johanneskoester commented Sep 14, 2015

Good to know! Maybe we can invite Brad to migrate their stuff once we have reached a critical mass with Bioconda.

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hyeshik Sep 15, 2015

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@johanneskoester Thank you! I just created an account on anaconda.org.

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hyeshik commented Sep 15, 2015

@johanneskoester Thank you! I just created an account on anaconda.org.

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johanneskoester Sep 15, 2015

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Great. Added you!

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johanneskoester commented Sep 15, 2015

Great. Added you!

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hyeshik Sep 16, 2015

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@johanneskoester I seems that I don't have a permission to write the recipes github repo. Can I get one? Thank you!

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hyeshik commented Sep 16, 2015

@johanneskoester I seems that I don't have a permission to write the recipes github repo. Can I get one? Thank you!

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johanneskoester Sep 16, 2015

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Of course. Sorry for that, does it work now?

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johanneskoester commented Sep 16, 2015

Of course. Sorry for that, does it work now?

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It works. Thank you!

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hyeshik commented Sep 16, 2015

It works. Thank you!

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@johanneskoester, I am enthusiastic about this idea as well, especially since I've been using wonky Makefiles to deal with software environments for my company =) I'd love to contribute in any way possible, although I don't have much experience with conda apart from being an end-user. My anaconda.org account is dkoppstein.

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dkoppstein commented Sep 24, 2015

@johanneskoester, I am enthusiastic about this idea as well, especially since I've been using wonky Makefiles to deal with software environments for my company =) I'd love to contribute in any way possible, although I don't have much experience with conda apart from being an end-user. My anaconda.org account is dkoppstein.

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johanneskoester Sep 24, 2015

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Hi,
glad to hear that you want to join us, thanks! Conda packaging is really easy. Basically, it is just some metadata plus a shell script with the commands you would use if you install a tool manually.

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johanneskoester commented Sep 24, 2015

Hi,
glad to hear that you want to join us, thanks! Conda packaging is really easy. Basically, it is just some metadata plus a shell script with the commands you would use if you install a tool manually.

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Johannes;
This is a great initiative, thank you for putting it together. I'd love to contribute as well. We have a lot of packages prepared for bcbio dependencies and could happily move over to more community driven packaging:

https://anaconda.org/bcbio

It may also be worth getting in touch with the CGAT folks, who have a wide variety of conda tools as well:

https://anaconda.org/cgat

What Linux platform do you target builds for? In bcbio we need to support people running on older platforms so build everything in a CentOS5 docker container. We have a ready to run script that does this, only re-building new recipes that are missing from anaconda.org:

https://github.com/chapmanb/bcbio-conda#readme

Thanks again for organizing this.

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chapmanb commented Sep 25, 2015

Johannes;
This is a great initiative, thank you for putting it together. I'd love to contribute as well. We have a lot of packages prepared for bcbio dependencies and could happily move over to more community driven packaging:

https://anaconda.org/bcbio

It may also be worth getting in touch with the CGAT folks, who have a wide variety of conda tools as well:

https://anaconda.org/cgat

What Linux platform do you target builds for? In bcbio we need to support people running on older platforms so build everything in a CentOS5 docker container. We have a ready to run script that does this, only re-building new recipes that are missing from anaconda.org:

https://github.com/chapmanb/bcbio-conda#readme

Thanks again for organizing this.

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johanneskoester Sep 25, 2015

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Hi Brad,
I'm very glad you want to join. We already thought about contacting you. Great work with the bcbio. So, feel free to move stuff over!
Regarding the builds, that is a very good question. So far, my impression was that if we target e.g. linux-64 and include all dependencies for build and run as conda packages, the resulting builds should be independent of the underlying linux platform. E.g. conda is shipping its own libstdc++ etc, right?
Am I missing something here?

Best,
Johannes

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johanneskoester commented Sep 25, 2015

Hi Brad,
I'm very glad you want to join. We already thought about contacting you. Great work with the bcbio. So, feel free to move stuff over!
Regarding the builds, that is a very good question. So far, my impression was that if we target e.g. linux-64 and include all dependencies for build and run as conda packages, the resulting builds should be independent of the underlying linux platform. E.g. conda is shipping its own libstdc++ etc, right?
Am I missing something here?

Best,
Johannes

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Johannes;
Thanks so much for including me. Regarding builds, unfortunately it is not that isolated. You'll compile against system packages which will cause failures on different systems. glibc is the most common cause of these. For instance, the current bedtools build fails to run on CentOS6:

~/test/anaconda/bin/bedtools 
/cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by /cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools)
/cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools)

This is the same issue you're seeing in #2.

The anaconda folks build their packages on CentOS5 which avoids most of these issues (although they still do get system-specific things -- the curl package doesn't work on non-RedHat systems due to certificate differences). With a CentOS5 based automated build you can avoid the most common compatibility issues and I haven't had any problems with portability of packages so far. I could replicate the setup we have in bcbio-conda here if that would help.

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chapmanb commented Sep 25, 2015

Johannes;
Thanks so much for including me. Regarding builds, unfortunately it is not that isolated. You'll compile against system packages which will cause failures on different systems. glibc is the most common cause of these. For instance, the current bedtools build fails to run on CentOS6:

~/test/anaconda/bin/bedtools 
/cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by /cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools)
/cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cm/shared/apps/bcbio/20141204-devel/data/anaconda/bin/bedtools)

This is the same issue you're seeing in #2.

The anaconda folks build their packages on CentOS5 which avoids most of these issues (although they still do get system-specific things -- the curl package doesn't work on non-RedHat systems due to certificate differences). With a CentOS5 based automated build you can avoid the most common compatibility issues and I haven't had any problems with portability of packages so far. I could replicate the setup we have in bcbio-conda here if that would help.

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Hi Brad,
thanks for the insight! But what about packages like glibc. If you manage to build against that, wouldn't bedtools work on all platforms, regardless of the system glibc?

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johanneskoester commented Sep 25, 2015

Hi Brad,
thanks for the insight! But what about packages like glibc. If you manage to build against that, wouldn't bedtools work on all platforms, regardless of the system glibc?

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Oh, I have just seen that this package just seems to copy the system libs. Strange...
Ok, in this case, it would be great if you could replicate your CentOS setup for us, thank you!

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johanneskoester commented Sep 25, 2015

Oh, I have just seen that this package just seems to copy the system libs. Strange...
Ok, in this case, it would be great if you could replicate your CentOS setup for us, thank you!

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Alternatively, we could try to get the binstar builds up and running. I experimented a bit with them, but I never managed to trigger a build. I can only submit them, but they don't seem to be assigned to a build queue.

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johanneskoester commented Sep 25, 2015

Alternatively, we could try to get the binstar builds up and running. I experimented a bit with them, but I never managed to trigger a build. I can only submit them, but they don't seem to be assigned to a build queue.

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@johanneskoester, do you envision this being Linux-64 only or also Mac/Windows? If the latter, perhaps it makes sense to try to appropriate funds for organization status so we can use those types of build nodes (assuming we can get binstar to work).

FWIW I'm totally fine with it being Linux-64 only.

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dkoppstein commented Sep 25, 2015

@johanneskoester, do you envision this being Linux-64 only or also Mac/Windows? If the latter, perhaps it makes sense to try to appropriate funds for organization status so we can use those types of build nodes (assuming we can get binstar to work).

FWIW I'm totally fine with it being Linux-64 only.

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I think linux is most important. I have uploaded some MacOS X builds because I need them for a Snakemake tutorial I am giving. But in general, I would say we should start with Linux and see where the journey takes us.

I would propose the following plan:

  1. Build for linux-64/CentOS 5 with Brad's setup.
  2. Once the automated binstar builds work, build for linux-64 via the binstar queue.
  3. Depending on user requests, decide at some point if there is a market for extending builds to MacOS X.

I think I won't go for Windows, because many tools don't support it at all. I also don't want to encourage people to use Win for bioinformatics ;-).

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johanneskoester commented Sep 25, 2015

I think linux is most important. I have uploaded some MacOS X builds because I need them for a Snakemake tutorial I am giving. But in general, I would say we should start with Linux and see where the journey takes us.

I would propose the following plan:

  1. Build for linux-64/CentOS 5 with Brad's setup.
  2. Once the automated binstar builds work, build for linux-64 via the binstar queue.
  3. Depending on user requests, decide at some point if there is a market for extending builds to MacOS X.

I think I won't go for Windows, because many tools don't support it at all. I also don't want to encourage people to use Win for bioinformatics ;-).

chapmanb added a commit that referenced this issue Sep 26, 2015

Scripts and instructions for automated builds (#1)
- An automated script that checks for out of date packages,
  builds them and uploads to anaconda.org.
- A shell script to build Linux packages inside a Docker CentOS5
  container for portability across Linux platforms.
- Update README with instructions on use.
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Johannes and David;
Thanks for the thoughts on the build ideas. I pushed scripts which we can use for building and uploading packages on Linux and MacOSX. For Linux, it uses a CentOS 5 docker container which will provide hopefully widely compatible binaries. For MacOSX, we should just build directly on a Mac machine but this will require marking tools that don't build on Mac, or where the recipe uses Linux binaries.

I would love to eventually use the anaconda.org builds, but explored this a year ago and didn't have any luck getting it set up, even with offering to pay for build boxes. I got the feeling it's still under development on their side but the situation could have changed in the interim.

Let me know if you have any problems running the scripts, I'm happy to improve the docs or scripts as needed. Thanks again.

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chapmanb commented Sep 26, 2015

Johannes and David;
Thanks for the thoughts on the build ideas. I pushed scripts which we can use for building and uploading packages on Linux and MacOSX. For Linux, it uses a CentOS 5 docker container which will provide hopefully widely compatible binaries. For MacOSX, we should just build directly on a Mac machine but this will require marking tools that don't build on Mac, or where the recipe uses Linux binaries.

I would love to eventually use the anaconda.org builds, but explored this a year ago and didn't have any luck getting it set up, even with offering to pay for build boxes. I got the feeling it's still under development on their side but the situation could have changed in the interim.

Let me know if you have any problems running the scripts, I'm happy to improve the docs or scripts as needed. Thanks again.

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I would like to join!

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tomkinsc commented Oct 1, 2015

I would like to join!

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sauloal Oct 1, 2015

Hey,

I think reproducibility is a hot topic now. We are also working on a similar project: https://github.com/BioDocker/biodocker

Apparently there's a huge double work here (and we are not the only ones).

It would be interesting to partner and for sure we could install your conda packages inside our docker images instead of downloading from source, reducing the download size.

Also, could you please tell me what are the advantages of conda over docker? I've personally never used it but the multiplatform nature and no "mount/port forward/etc" crap seem very nice.

regards

sauloal commented Oct 1, 2015

Hey,

I think reproducibility is a hot topic now. We are also working on a similar project: https://github.com/BioDocker/biodocker

Apparently there's a huge double work here (and we are not the only ones).

It would be interesting to partner and for sure we could install your conda packages inside our docker images instead of downloading from source, reducing the download size.

Also, could you please tell me what are the advantages of conda over docker? I've personally never used it but the multiplatform nature and no "mount/port forward/etc" crap seem very nice.

regards

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The biggest disadvantage for me personally is that Docker is not allowed on our HPC cluster! In contrast, conda installs everything in my home directory without the need for any elevated privileges.

Conda is mostly for installing executables and libraries. You can't do things like run an isolated mysql server using conda. But that's exactly the sort of thing docker is good at.

While conceptually there's a lot of overlap between the projects, it looks like there's not much domain overlap yet: biodocker has lots of proteomic packages while bioconda has lots of sequencing packages. One way to minimize duplicated work while taking advantage of both projects would be to 1) port existing dockerfiles into conda packages under bioconda and then 2) pull conda packages into docker containers built under biodocker.

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daler commented Oct 1, 2015

The biggest disadvantage for me personally is that Docker is not allowed on our HPC cluster! In contrast, conda installs everything in my home directory without the need for any elevated privileges.

Conda is mostly for installing executables and libraries. You can't do things like run an isolated mysql server using conda. But that's exactly the sort of thing docker is good at.

While conceptually there's a lot of overlap between the projects, it looks like there's not much domain overlap yet: biodocker has lots of proteomic packages while bioconda has lots of sequencing packages. One way to minimize duplicated work while taking advantage of both projects would be to 1) port existing dockerfiles into conda packages under bioconda and then 2) pull conda packages into docker containers built under biodocker.

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sauloal Oct 1, 2015

@daler I see. Thank you very much. I was also struggling on how to run the programs on our HPC too. this is great.

BTW. indeed the initial creators are from the proteomics field but I'm from the genomics and I've started porting several programs:
https://github.com/BioDocker/sandbox

I really like the idea to create packages here and installing them inside docker. makes the docker images lighter and the same package can be used inside docker, outside docker and in HPC. 3 in one.

I like this idea very much. We'll keep talking.

sauloal commented Oct 1, 2015

@daler I see. Thank you very much. I was also struggling on how to run the programs on our HPC too. this is great.

BTW. indeed the initial creators are from the proteomics field but I'm from the genomics and I've started porting several programs:
https://github.com/BioDocker/sandbox

I really like the idea to create packages here and installing them inside docker. makes the docker images lighter and the same package can be used inside docker, outside docker and in HPC. 3 in one.

I like this idea very much. We'll keep talking.

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Hi Johannes,

great initiative, I'd be pleased to chip in. I recently started using conda and I haven't gotten round to learning how to build packages, but looking at your recipes should help.

Cheers,

Per

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percyfal commented Oct 3, 2015

Hi Johannes,

great initiative, I'd be pleased to chip in. I recently started using conda and I haven't gotten round to learning how to build packages, but looking at your recipes should help.

Cheers,

Per

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Hi @percyfal, @tomkinsc and @sauloal,
Glad to hear that you are interested in the project!
I have invited you to the github team. I can also provide access to the corresponding anaconda team if you give me your anaconda.org usernames. The latter is not urgent, we should soon have automatic builds so that direct interaction with anaconda might be rarely needed.

@sauloal: indeed, BioDocker sounds like a perfect complement for bioconda! I would be extremely happy to cooperate and advertise the two together!

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johanneskoester commented Oct 5, 2015

Hi @percyfal, @tomkinsc and @sauloal,
Glad to hear that you are interested in the project!
I have invited you to the github team. I can also provide access to the corresponding anaconda team if you give me your anaconda.org usernames. The latter is not urgent, we should soon have automatic builds so that direct interaction with anaconda might be rarely needed.

@sauloal: indeed, BioDocker sounds like a perfect complement for bioconda! I would be extremely happy to cooperate and advertise the two together!

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I have been doing this for my groups stuff for a while! Glad to see a organized effort somewhere!

I would love to contribute the packages I have built that are not already represented! Please add me to the team!

Gus

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xguse commented Oct 5, 2015

I have been doing this for my groups stuff for a while! Glad to see a organized effort somewhere!

I would love to contribute the packages I have built that are not already represented! Please add me to the team!

Gus

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Great, thanks for adding me @johanneskoester. My username on anaconda is percyfal.

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percyfal commented Oct 5, 2015

Great, thanks for adding me @johanneskoester. My username on anaconda is percyfal.

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johanneskoester Oct 5, 2015

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Welcome Gus! Do you have the same username on anaconda.org? Then I can add you to the team there as well.

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johanneskoester commented Oct 5, 2015

Welcome Gus! Do you have the same username on anaconda.org? Then I can add you to the team there as well.

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@johanneskoester : no I am gusdunn on anaconda.org. Thanks again!

Gus

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xguse commented Oct 6, 2015

@johanneskoester : no I am gusdunn on anaconda.org. Thanks again!

Gus

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johanneskoester Oct 6, 2015

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ok, added!

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johanneskoester commented Oct 6, 2015

ok, added!

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roryk Oct 20, 2015

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Thanks for setting this up everyone, can I help out? I'm roryk on anaconda.org and here.

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roryk commented Oct 20, 2015

Thanks for setting this up everyone, can I help out? I'm roryk on anaconda.org and here.

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johanneskoester Oct 20, 2015

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Welcome! I have added you to the teams.

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johanneskoester commented Oct 20, 2015

Welcome! I have added you to the teams.

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kyleabeauchamp Oct 23, 2015

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The docs seem to suggest that people need to join the team to contribute, but I wonder if it makes sense to encourage people to file pull requests as well? AFAIK that seems like the easiest path to making a contribution.

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kyleabeauchamp commented Oct 23, 2015

The docs seem to suggest that people need to join the team to contribute, but I wonder if it makes sense to encourage people to file pull requests as well? AFAIK that seems like the easiest path to making a contribution.

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johanneskoester Oct 23, 2015

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Good idea, I have added a sentence about that (in case somebody does not want to be a permanent team member).

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johanneskoester commented Oct 23, 2015

Good idea, I have added a sentence about that (in case somebody does not want to be a permanent team member).

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youqi1989 Jul 28, 2018

Hi Bioconda team! I'd like to join too.

I have fixed the PR here #10106. This is my first time for Contributing a recipe. Could you please check again?@bgruening

youqi1989 commented Jul 28, 2018

Hi Bioconda team! I'd like to join too.

I have fixed the PR here #10106. This is my first time for Contributing a recipe. Could you please check again?@bgruening

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RickGelhausen Jul 30, 2018

Hi, I want to contribute. Please add me.

RickGelhausen commented Jul 30, 2018

Hi, I want to contribute. Please add me.

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apcamargo Jul 30, 2018

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Hi, I'd like to be join as a contributor!

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apcamargo commented Jul 30, 2018

Hi, I'd like to be join as a contributor!

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bgruening Jul 30, 2018

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Welcome @RickGelhausen @apcamargo @youqi1989!
@youqi1989 I checked again but your PR removes files that are needed and adds files that are not needed.

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bgruening commented Jul 30, 2018

Welcome @RickGelhausen @apcamargo @youqi1989!
@youqi1989 I checked again but your PR removes files that are needed and adds files that are not needed.

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Hi, I'd also like to join as a contributor.

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t-neumann commented Aug 2, 2018

Hi, I'd also like to join as a contributor.

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@t-neumann, welcome to the team!

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bgruening commented Aug 2, 2018

@t-neumann, welcome to the team!

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I would like to join the team now that my PR #10089 is passing tests.

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holmrenser commented Aug 2, 2018

I would like to join the team now that my PR #10089 is passing tests.

aryakaul added a commit to aryakaul/bioconda-recipes that referenced this issue Aug 3, 2018

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Hello all, I would also like to join the team now that my PR #10250 is passing the tests. Thanks!

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aryakaul commented Aug 3, 2018

Hello all, I would also like to join the team now that my PR #10250 is passing the tests. Thanks!

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Hi, I would like to join as a contributor.

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haghshenas commented Aug 4, 2018

Hi, I would like to join as a contributor.

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Hi, I'd like to be join as a contributor!

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pb-cdunn commented Aug 4, 2018

Hi, I'd like to be join as a contributor!

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@holmrenser, @aryakaul, @haghshenas, @pb-cdunn; welcome to the team!

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bgruening commented Aug 5, 2018

@holmrenser, @aryakaul, @haghshenas, @pb-cdunn; welcome to the team!

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@bgruening thank you! Can I merge my PR (#10250) now, or should I wait for it to be merged by others since it's my first one?

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aryakaul commented Aug 5, 2018

@bgruening thank you! Can I merge my PR (#10250) now, or should I wait for it to be merged by others since it's my first one?

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smussmann82 Aug 5, 2018

Hello, I would like to join as a contributor.

smussmann82 commented Aug 5, 2018

Hello, I would like to join as a contributor.

aryakaul added a commit that referenced this issue Aug 5, 2018

NovaSplice (#10250)
* attempt #1 to add novasplice recipe

* novasplice

* Update meta.yaml
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Welcome @smussmann82!

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bgruening commented Aug 5, 2018

Welcome @smussmann82!

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lkuchenb Aug 6, 2018

Please add me to the team.

lkuchenb commented Aug 6, 2018

Please add me to the team.

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Hi, I would like to be join as a contributor!

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chienchi commented Aug 7, 2018

Hi, I would like to be join as a contributor!

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Hi @lkuchenb & @chienchi! Welcome to Bioconda!

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bgruening commented Aug 7, 2018

Hi @lkuchenb & @chienchi! Welcome to Bioconda!

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cdunn2001 Aug 8, 2018

Please add me to the team!

cdunn2001 commented Aug 8, 2018

Please add me to the team!

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Hello, please add me!

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skrakau commented Aug 8, 2018

Hello, please add me!

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sharbie88 Aug 9, 2018

Hi, new to this. Please add me to the team. :)

sharbie88 commented Aug 9, 2018

Hi, new to this. Please add me to the team. :)

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willemdek11 Aug 9, 2018

Hi, I would like to work together with my colleague on the plasflow recipe, could you add me to the team?

willemdek11 commented Aug 9, 2018

Hi, I would like to work together with my colleague on the plasflow recipe, could you add me to the team?

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Hi @cdunn2001, @skrakau, @sharbie88 and @willemdek11! Welcome to Bioconda!

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bgruening commented Aug 12, 2018

Hi @cdunn2001, @skrakau, @sharbie88 and @willemdek11! Welcome to Bioconda!

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alexeigurevich Aug 13, 2018

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Hi, I would like to join (mostly for updating QUAST recipes, especially for cases when we release minor updates). Thanks!

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alexeigurevich commented Aug 13, 2018

Hi, I would like to join (mostly for updating QUAST recipes, especially for cases when we release minor updates). Thanks!

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@alexeigurevich welcome to the Bioconda community!

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bgruening commented Aug 13, 2018

@alexeigurevich welcome to the Bioconda community!

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Hi, I would like to join. I am now working on adding VarGeno into bioconda, and plan to add more of my bioinformatics tools into bioconda.

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bbsunchen commented Aug 13, 2018

Hi, I would like to join. I am now working on adding VarGeno into bioconda, and plan to add more of my bioinformatics tools into bioconda.

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Welcome @bbsunchen!

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bgruening commented Aug 14, 2018

Welcome @bbsunchen!

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handetopa Aug 14, 2018

Hi, I would like to join as a contributor too. Could you please add me to the team? Thanks in advance!

handetopa commented Aug 14, 2018

Hi, I would like to join as a contributor too. Could you please add me to the team? Thanks in advance!

asmariyaz23 added a commit that referenced this issue Aug 14, 2018

Trinity (#10419)
* add convert_zero_one_based (#10001)

* add convert_zero_one_based
* remove unecessary tests
* test import

* Gembs (#10109)

* gembs: passes a mulled build
* correcting dependencies
* gembs: passes a mulled build
* correcting dependencies
* pointing to the current gem3-mapper instead of a custom version
* removing openssl
* gembs: passes a mulled build
* correcting dependencies
* pointing to the current gem3-mapper instead of a custom version
* removing openssl
* starting build at 0
* Changing to the main repository instead of the testing fork

* Update sevenbridges-python recipe to 0.15.0 (#10113)

* update to new version (#10015)

* update to new version

the old version had a bug whereby some reads were dropped. See mourisl/Rcorrector#12

* remove recipe from blacklist

* Update meta.yaml

* try adding flags

per comment from @jpuritz

* fix makefile

* bump for alevin hotfix (#10118)

* bump for alevin hotfix

* Update meta.yaml

Put md5sum for the zip, not .tar.gz.  Correct that.

* Bump JBrowse version to 1.15.0 (#10116)

Add missing dependency perl-io-uncompress-gunzip.

Support osx.

* Update krocus to v0.2.3 (#10115)

*  updating to ragout v2.1, should fix the problem with inconsistent ... (#10105)

* updating to ragout v2.1, should fix the problem with inconsistent newick package versions

* Dialign2 (#10098)

* Started work on dialign2

* Fixing build/host

* compiler

* still compiler error

* still

* still working on compiler

* should be fixed

* Fixed typo

* desperate measures

* typo

* whatever

* Update meta.yaml

* fix hash

* freaky circleci, please run

* working on paths and exports

* still working on paths and exports

* still working on paths

* last fixes

* verylast fixes

* verylast fixes?

* wtf circleci

* wtf circleci aber echt

* Fixing license

* Working

* env vars export

* Working on postlink

* Working on prelink

* Working on env vars

* Done?

* skipping osx and done i hope

* Added pre-unlink and added DOI

* Fixing exports

* Removed unnecessary scripts, added wrapper

* Added patch and sed workaround for env var DIALIGN2_DIR

* Fixing sed command

* Fixing sed command again

* I hate sed

* fixed typo and eyecandy

* Remove various packages from the blacklist (#10117)

* Remove various packages from the blacklist

* eqtlbma needs to always have openblas included

* Patch mamotif so it uses matplotlib.use('Agg') early on

* Skip eqtlbma on OSX due to openmp

* Add r-bipartite (#10119)

* Add r-bipartite

* removed 2nd url

* Add r-phylomeasures (#10120)

* Add r-phylomeasures

* removed 2nd url

* Bump perl-file-path (#10123)

* Bump perl-file-path

* Small fixes

* Fix 2 perl packages (#10124)

* bump pysam (#10126)

* Update primer3 to v2.4.0 (#10122)

* Update primer3 to v2.4.0

* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
* [ ] This PR adds a new recipe.
* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
* [x] This PR updates an existing recipe.
* [ ] This PR does something else (explain below).

Bump primer3 to `v2.4.0`.

* Review fixups for Update primer3 to v2.4.0

* R phylosignal (#10128)

* Add r-phylosignal

* Removed fn:

* removed all win

* fixed meta.yaml; ade4 now updated to 1.7_11

* R coenocliner (#10127)

* Add r-coenocliner

* modified maintainers

* add msisensor (#10092)

* add msisensor

* skip macos

* change include and lib

* fix ncurse

* add tinfo

* add cpath

* add LIBRARY_PATH

* Update to fastp v0.19.3 (#10131)

This version provides a fix for possible deadlock on cloud-based docker env.

* Add r-ggrasp (#10129)

* Add r-ggrasp

* trivial change to restart checks now the r-bgmm is on conda-forge

* updated r-nodiv recipe; unblacklisted (#10132)

* Blood moon blaclist changes (#10133)

* remove a few things from the blacklist

* Try something for osx

* skip xatlas on osx

* Fix two more perl (#10135)

* Fix perl-image-size

* Fix perl-aceperl

* Add perl-cache-cache

* Add perl-ipc-sharelite

* Add perl-digest-sha1

* bumping to 0.7.1 (#10136)

* Remove packages from the blacklist (#10134)

* Remove packages from the blacklist

* Fix fermi on osx I hope

* Ah, only gnu assumes inline functions are static

* preseq 2.0.3 includes the wrong header for proper building on newer OSX versions. Try to cxxflags around this.

* Skip preseq on OSX, clang doesn't like the older headers

* Added recipe prototype for pymisc-utils (#10139)

* Added recipe prototype for pymisc-utils

* Updated build dependencies

* Updated repo url

* Fixed copying of executables

* Added dependency

* Minor fix

* Skip python 2

* Idr (#10112)

* idr: push version to 2.0.4.2

* OMERO.py 5.4.7 (#10138)

* OMERO.py 5.4.7

* Bump version in setup.py to 5.4.7

* Update EMA to v0.6.2 (#10141)

* Add r-htssip (#10121)

* Add r-htssip

* converted r- to bioconductor-

* trivial change to restart checks

* Ragout 2.1.1 (#10144)

* ragout 2.1.1 update (now as a Python package)

* Riboseed updates (#10143)

* [wip] riboseed add quast and networkx

* update build number

* bump version, remove dep on pyutilsnrw

* [wip]  remove quast (single tear), which isn't built for py3 on conda

* bump version

* bump version to fix cmdline args

* updating cromwell to 0.34 (#10145)

* updating cromwell to 0.34

* gembs, rebuild (#10140)

removing restrictions on python beyond build-skip. matplotlib not needed for building

* PacBio: bump lima to 1.7.0 (#10151)

* gembs: adding missing runtime dependencies and moving build script to meta file (#10150)

* Jcvi python module (#10152)

* add jcvi recipe

* fixes

* update biokit to v0.4.4 (#10148)

* update biokit to v0.4.4

* Jcvi is python 2 only (#10153)

* jcvi is python 2 only

* negation bug in my head

* changed to 1.0.6 (#10157)

* updated bbmap to 38.16 (#10159)

* forgi: loosened the dependencies (#10156)

* Grid6 (#10158)

* changed to 1.0.6

* changed to veersion 1.0.6

* Update biohansel to v2.1.0 (#10160)

* Update biohansel to v2.1.0

* Python 3.6 builds only

* Update meta.yaml

* Fixing perl-json-xs and deps (#10161)

* Fix perl-common-sense

* Fix perl-types-serialiser

* Bump perl-canary-stability

* Bump perl-json-xs

* Unblacklist

* Small fixes

* Build perl-json-xs later

* Unblacklist perl-json-xs (#10163)

* PIPITS 2.2 update. (#10164)

* Perl OS X fixes 20180731 (#10165)

* Various perl OS X fixes.

* Remove perl-parallel-forkmanager from blacklist.

* Riboseed updates (#10162)

* [wip] riboseed add quast and networkx

* update build number

* bump version, remove dep on pyutilsnrw

* [wip]  remove quast (single tear), which isn't built for py3 on conda

* bump version

* bump version to fix cmdline args

* bump version

* Update meta.yaml

* Unblacklist 2 more perl  (#10166)

* Unblacklist 2 perl

* Unblacklisting

* Fix typo

* alfred v0.1.8 (#10168)

* bump build numbers for htslib dependent recipes.

* PacBio: Update `pbcommand` to 1.1.1 (#10172)

* PacBio: Update `pbcore` to 1.5.1 (#10173)

* Remove obsolete build script.

* PacBio: Remove `pbcommand` from build-fail-blacklist (#10176)

* PacBio: Initial addition of `pbcoretools` (#10169)

* bump htslib to get libdeflate pinning

* 2.1.3 update (#10180)

* updated bbmap to 38.18 (#10178)

* snakemake 5.2.2 (#10179)

* snakemake 5.2.2

* add python as run dependency.

* Chado tools (#9991)

* bioconda recipe for chado-tools
* use meta.yaml created by skeleton
* set source to github
* remove build script section
* remove import section
* restore import section
* correction
* noarch: python

* Update mob_suite to 1.4.6 (#10088)

* Update mob_suite to 1.4.6
* Update sha256

* added recipe for itsxpress 1.6.4 (#10099)

* Enable python3.6 build (#10101)

This recipe should not skip py36, as version 4.0.3 of RGI primarily supports Python3. This change will enable rgi to work in Python3 environments.

* bump phyluce to 1.6.6 (#10114)

* bump phyluce to 1.6.6
* adding DOI

* Update breseq to v0.33.0 (#10175)

* Update breseq to v0.33.0

* add disable-compiler-version-check.patch

* Update meta.yaml

* Dropseq tools (#10170)

* first attempt

* package name now lowercase

* test command gave an exit 1

* another try

* try..

* missed a slash

* wrong test to test

* qutoe

* finalizing recipe before push

* last test

* add a test on help

* added test for each command

* Add deepsvr (#10167)

* add deepsvr

* switch install to pip

* test cli entry point in build

* update sha

* update sha

* update sha

* Test help command

* Remove command test

* Add command test

* Perl OS X fixes 20180801 (#10184)

* More perl fixes for OS X.

* Remove unneeded dependency.

* Update schema-salad to 2.7.20180731120629 (#10195)

* Update gatk4 to 4.0.7.0 (#10191)

* Update toulligqc to v0.10 (#10192)

* Update gridss to v1.8.0 (#10193)

* Update dxpy to v0.257.3 (#10197)

* Update anndata to 0.6.6 (#10186)

* Update anndata to 0.6.6

* python >=3

* require python >=3.5

* Update isatools to v0.10.2 (#10190)

* Update chado-tools to v0.0.4 (#10189)

* enabled jni; bumped version to 38.19 . (#10185)

* enabled jni; bumped version to 38.19 .

* construct test file on the fly

* use already-installed resource file for testing

* added nodisk to avoid creating leftover files after test

* changed tests to what blast does

* fixed filenames

* another filename fix

* dropped pipefail

* Update mglex to v0.2.1 (#10188)

* Update mglex to v0.2.1

* update meta.yaml

* New: wes-service client only (#10200)

Provides a client for Workflow Execution Service (WES) endpoints,
part of the GA4GH initiative.

* Riboseed updates (#10202)

* [wip] riboseed add quast and networkx

* update build number

* bump version, remove dep on pyutilsnrw

* [wip]  remove quast (single tear), which isn't built for py3 on conda

* bump version

* bump version to fix cmdline args

* bump version

* bump version

* 2.1.4 release (#10204)

* trigger rebuild

* Trinotate: fix error in Build_Trinotate_Boilerplate_SQLite_db.pl (#10205)

* fix path error in Build_Trinotate_Boilerplate_SQLite_db.pl

* patch trinotate_report_summary.pl too

* Move PyVCF to conda-forge (#9979)

* Add recipe for hotspot3d 0.6.0. (#10209)

* Fasttreecondbuild3 (#10177)

* remove FastMP test

* add SRC_DIR and filename to build script and move MP into linux-specific build

* remove fasttree from blacklist

* update older versions as well

* trigger rebuild

* bump build versions

* change the tests so that they end

* Update WGCNA to 1.63 (#10203)

* phantompeakqualtools first commit (#10171)

* phantompeakqualtools first commit

* add in r-spp dependency

* correcting dependencies

* Updated ont-tombo to version 1.4. (#10182)

* Updated ont-tombo to version 1.4.

* Removed setuptools from run requirements.

* Added extra identifier to the bioarxiv pre-print.

* Update meta.yaml

* Update pycoqc to 1.1.alpha3 (#10198)

* Update pycoqc to 1.1.alpha3

* add noarch: python

* remove universal binaries for ViennaRNA (#10043)

* remove universal binaries for ViennaRNA

* the flag in configure causes a 1.33-2.00x slowdown (docs say it
interferes with some link-time optimizations)
* the flag is unnecessary since its intent was to bind with Apple's
stock python distribution (rather than conda)

echo 'GCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA\nGCGCUUCGCCGCGCGCC&GCGCUUCGCCGCGCGCA' | time RNAcofold --noPS -p

RNAcofold --noPS -p  0.02s user 0.00s system 89% cpu 0.030 total

RNAcofold --noPS -p  0.01s user 0.00s system 74% cpu 0.022 tota

* bump buildno to trigger build

* Bump libsequence to 1.9.4.  Update dependencies, which are build-only! (#10210)

* Bump libsequence to 1.9.4.  Update dependencies, which are build-only!
Compiler and run unit tests after build.

* skip os x for now.  the case-sensitivity of the file system makes building impossible until we get closer to libseq 2.0

* Unblacklist perl-file-find-rule (#10218)

* unblacklist perl-file-find-rule

* workaround from conda/conda-build#2824

* Fix python dependency for Stacks 2.1 and remove Stacks dependency from dDocent (#10213)

* remove python spec

* remove python

* remove python

* remove stacks dependency from dDocent

* Update meta.yaml

* Add deepbinner. (#10111)

* Add deepbinner.

* overwrite numpy pinning because tensorflow needs a newer version.

* rebuild htslib in the hope that libdeflate pinning is now included on linux as well.

* add suport for centroid rna package (#9647)

* add suport for centroid rna package

* add suport for centroid rna package

* linting fail - fix by removing fn name

* Change test from python to sh script.

* Change test from python to sh script.

* skiping osx, reintroducing python based test (simple check of output code not reliable)

* add doi identifiers

doi iderntifiers directly related to programs contained in package

* run test from meta with grep instead of run_test.py


add py2k to skip

per request adding py2k to skip

* suppress output of the test commands

* unblacklist perl-dbi (#10236)

* unblacklist perl-dbi

* permission problem with fix_shebang

* chmod again

* Update r-wgcna build

* Update build number

* Fix macs2 recipe (#10232)

* New recipe: Slamdunk (#10199)

* Slamdunk recipe setup.

* No fixed java version.

* Java-jdk -> Openjdk.

* PREFIX removed from recipe.

* wget dependency added.

* conda build checking.

* path extensions.

* Only py2.7 requirement.

* Win skip removed.

* lka

* lkal

* pip install switch

* samtools dependencies added

* senf

* senf1

* recent

* satool

* sha

* shaupdate

* freaky

* testy

* testz

* Slamdunk v0.3.1 bioconda build 0.

* SHA256 updated.

* Skipping py3 build. Using pip.

* Python3 builds not skipped - otherwise package will not be built at all.

* OSX build deactivated.

* Skip py3k. OSX activated.

* OSX deactivated for good.

* .buildkite restored. Skip merged into one-liner.

* Unblacklist perl-dbd-sqlite (#10239)

* Unblacklist perl-dbd-sqlite

* permission problem

* Update treetime to v0.4.1 (#10229)

* Update nglview to v1.1.5 (#10217)

* Unblacklist trinotate recipe (#10206)

* unblacklist trinotate

* this module needs to be rebuilt

* fix broken recipe

* fix find command

* rebuild

* permission problem

* Update build.sh

* python-chado 2.1.5 (#10246)

* Add recipe for connectome-workbench 1.3.1. (#10248)

* Add recipe for connectome-workbench 1.3.1.

* Use extended container.

* Update: wes-service-client, bcbio-variation-recall, bcbio (#10249)

- bcbio-variation-recall: Avoid use of gatk-framework. Fixes bcbio/bcbio-nextgen#2412
- wes-service-client: python2/3 fixes
- bcbio: RNA-seq CWL improvements

* Support osx. (#10251)

zlib not needed.

* Change compiler from c to cxx and bump build number. (#9900)

* Change compiler from c to cxx and bump build number.

* fix older recipes and remove fwdpp from blacklist

* reset build number

* blacklist old versions of fwdpp

* remove fwdpy11 from blacklist

* bump fwdpp to 0.6.1

* try not defining any environment variables related to compilation

* pull build fail blacklist from master

* include C compiler, too

* Update vt to 0.57721 (#10253)

* Trimmomatic update (#10257)

* update trimmomatic

* Update and rename trimmomatic.sh to trimmomatic.py

* Update build.sh

* Update meta.yaml

* Update trimmomatic.py

* remove old trimmomatic pkg

* Pairtools v0.2.0 (#10252)

* pairtools v0.2.0

* MultiQC version 1.6 release (#10254)

* MultiQC version 1.6 release

* Update meta.yaml

* Update meta.yaml

* bump version (#10258)

* adding recipe for lordfast (#10255)

* adding recipe lordfast

* adding c++ compiler

* Perl fix 11 (#10259)

* Bump perl-array-compare

* Fix perl-unicode-map

* Unblacklist

* Perl fix 12 (#10261)

* Add perl-module-loaded

* Add perl-graphics-colornames

* Fix perl-graphics-colorobject

* skesa 2.2-2 (#10262)

* Update shovill to 1.0.0 (#10256)

* Fastqe (#10245)

* Add fastqe

* Fix whitespace in description and noarch lint skip [lint skip should_be_noarch for recipes/fastqe]

* Add GeneNoteBook recipe (#10089)

* genenotebook recipe

* Build from prebundled tarball

* Bump perl-gd and add new dependency (#10260)

* Add perl-test-fork

* Bump perl-gd

* Revert extra deps

* NovaSplice (#10250)

* attempt #1 to add novasplice recipe

* novasplice

* Update meta.yaml

* Perl fix 13 (#10265)

* Bump perl-file-fetch

* Bump perl-file-sharedir-install

* Bump perl-file-sharedir

* Bump perl-html-tree

* Unblacklist

* Build perl-file-sharedir later

* Unblacklist perl-file-sharedir (#10267)

* Perl fix 14 (#10266)

* Add perl-padwalker

* Add perl-devel-cycle/

* Add perl-test-memory-cycle

* Fix perl-font-ttf

* Unblacklist

* Correct build numbe

* Correct build numbe

* Unblacklist perl-pdf-api2 (#10268)

* Fix perl-pdf-api2

* Unblacklist

* Remove various packages from the blacklist (#10269)

* Remove various packages from the blacklist

* graphmap uses openmp, which is problematic with clang

* Update bpipe to 0.9.9.6 (#10240)

* Update bpipe to 0.9.9.6

* Update meta.yaml

* add new commit to retrigger test

* use http instead of ftp (friendlier with travis) (#10272)

* gmap 2014.12.28 (#10181)

* gmap 2014.12.28

* added host section

* Update meta.yaml

* Add -ldeflate to gqt compile command. Add missing limit macro defintion to pindel compile command.

* Update: bcbio, bcbio-vm with WES support (#10274)

* ensure SIZE_MAX is defined.

* Fix flags.

* try setting variable as make argument

* set generic flags.

* Update sleuth to 0.30.0. (#10278)

* upgrade rscape (#10208)

* upgrade rscape

* glib

* clean then compile

* Update meta.yaml

* debug info

* relax plot version

* simplify test

* minor fix

* older versions

* older test

* even older

* even older

* no clean

* orig test

* bump version

* grep test

* working version

* bump working version

* Create conda_build_config.yaml

* clean then build

* v0.7.3

* upgrade rscape

* glib

* clean then compile

* Update meta.yaml

* debug info

* relax plot version

* simplify test

* minor fix

* older versions

* older test

* even older

* even older

* no clean

* orig test

* bump version

* grep test

* working version

* bump working version

* Create conda_build_config.yaml

* clean then build

* v0.7.3

* Update conda_build_config.yaml

* fix R2R makefile

* gxx config

* minor cleanup

* skip mac

* rnachipintegrator 1.1.0 (#10276)

* rnachipintegrator: update to version 1.1.0.

* Update meta.yaml

* Dialign fix, again (#10279)

* Fixing patch

* Increased build number

* Delete patchdialign.txt

* Clinker (#10244)

* Add clinker with wrapper

* Add full test

* Remove test data test as per guidelines

* Updated minimap2 to v2.12 (#10282)

* delly: update to fix boost linker error (#10283)

Trying to fix:
```
delly: symbol lookup error: delly: undefined symbol: _ZN5boost15program_options3argE
```
and seems like it might need a re-build after being unblacklisted.

* Unblacklist a few perl packages (#10275)

* unblacklist a few perl packages

* add back to blacklist temporarily

* add back temporarily

* another one

* trigger new test

* mac permissions

* reset build number [ci skip]

* mac permissions

* try to rebuild mac packages maybe

* damn, typo

* mac perms

* trigger new test

* trigger new test

* trigger

* Update mlst to 2.11 (#10263)

* Remove various packages from the blacklist (#10280)

* Remove various packages from the blacklist

* Tepid gave a rather tepid response

* update gubbins to a new version (#10289)

* Slamdunk package fix (#10290)

* Slamdunk recipe setup.

* No fixed java version.

* Java-jdk -> Openjdk.

* PREFIX removed from recipe.

* wget dependency added.

* conda build checking.

* path extensions.

* Only py2.7 requirement.

* Win skip removed.

* lka

* lkal

* pip install switch

* samtools dependencies added

* senf

* senf1

* recent

* satool

* sha

* shaupdate

* freaky

* testy

* testz

* Slamdunk v0.3.1 bioconda build 0.

* SHA256 updated.

* Skipping py3 build. Using pip.

* Python3 builds not skipped - otherwise package will not be built at all.

* OSX build deactivated.

* Skip py3k. OSX activated.

* OSX deactivated for good.

* .buildkite restored. Skip merged into one-liner.

* slamdunk v0.3.1 -> slamdunk v0.3.2 (Softlink fix).

* Update confindr to v0.3.3 (#10224)

* Update confindr to v0.3.3

* Update meta.yaml

* Delete build.sh

* Adding recipe for XHMM (#10183)

* Remove strainest, starseqr, strudel, and svtools from the blacklist (#10291)

* Build number updated. sha256 updated. (#10292)

* updates bwameth to 0.2.2 (#10293)

* Add setuptools as run dependency (needed by some helper). Add python as a host dependency, to work around problems with the metapackage. (#10294)

* adding recipe for hulk (#10295)

* nextflow 0.31.1 (#10296)

* nextflow 0.31.1

* reset build number

* Perl fix 15 (#10298)

* Fix perl-forks

* Fix perl-acme-damn

* Unblacklist

* Remove a few more perl recipes from blacklist (#10287)

* remove a few more perl recipes from blacklist

* temp disable

* we need perl-cgi on mac

* tab

* mac fixes

* various mac fixes

* fix lint missing_tests

* test

* modified the wrong recipe

* some broken perl osx packages

* Needed by perl-soap-lite

* perl-xml-twig dep problem

* damn... forgot this

* add back to blacklist until next batch

* mac permission

* mac rebuild

* fix hang

* perm problem

* blacklist for now

* Perl fix 16 (#10301)

* bump perl-excel-writer-xlsx

* Bump perl-archive-zip

* Unblacklist

* Bump perl-graphviz (#10303)

* Bump perl-test-inter (#10306)

* NanoSim-H 1.1.0.4 (#10307)

* NanoSim-H 1.1.0.4

* Update sha256

* Reset build nb

* flye 2.3.5 (#10309)

* Faqcs (#10300)

* adding recipe for FaQCs software

* update test command for R

* build change to number 1

* change R to r-base

* test for no R --version

* test redirect STDERR to STDOUT

* add R testing

* provide precomplied binary for MacOSX

* build number 1 -> 0

* make OPENMP=""

* nim-falcon (#10312)

* Update nasp to v1.1.2 (#10308)

* Update nasp to v1.1.2

* lint doi and skip noarch

* build linux only

* Update meta.yaml

* add recipe-maintainers

* update bbmap to 38.20; add doi for bbmerge; misc meta.yaml cleanup. (#10310)

* Rebuild older perl-json-xs (#10313)

* Rebuild older perl-json-xs

* fix permission on mac

* Unblacklist perl-lwp-protocol-https (#10304)

* unblacklist perl-lwp-protocol-https

* bump version

* requirement

* lint

* experimental patch

* disable tests

* fix

* perl-lwp-protocol-https fix (#10317)

* Update cyvcf2 to 0.10.0 (#10314)

* Update cyvcf2 to 0.10.0

* cyvcf2: add libcurl dependency

* PacBio: Update `lima` to 1.7.1 (#10318)

* PacBio: Update `isoseq3` to 3.0.0 (#10319)

* Perl: more unblacklisting (#10305)

* more unblacklisting

* graphviz

* fix

* mac build

* mac build

* perm

* rebuild on macos

* no need to rebuild this version (see #10313)

* mac perms

* rebuild

* rebuild

* PacBio: Initial addition of `pbsv` (#10320)

* Remove r-biclust in favour of the conda-forge one. (#10322)

* Unblacklist perl-soap-lite (#10324)

* unblacklist perl-soap-lite

* rebuild mac

* mac perms

* Bt2 build (#10328)

* Changes for building bowtie 2 static binaries

* Blank out LDFLAGS

* Update seven-bridges-python to 0.15.2 (#10330)

* Update CrossMap version (0.2.7 -> 0.2.8) (#10327)

* Update python-cluster to v1.4.1.post1 (#10222)

* Update python-cluster to v1.4.1.post1

* use pip

* Update loompy to 2.0.10 (#10214)

* Update loompy to 2.0.10

* Update meta.yaml

* noarch: python

* remove loompy from build-fail-blacklist

* Update meta.yaml

* Update gridss to v1.8.1 (#10331)

* Update catch to v1.1.0 (#10225)

* Update catch to v1.1.0

* add noarch and use pip

* Build cdbtools for osx (#10329)

* Update nanopolish recipe for 0.10.1 release (#10333)

* fixed flye build error (due to zlib) - package removed from blacklist (#10335)

* fixes #10336 (#10337)

* fixes 10336

* increase build number and add test

* Update meta.yaml

* tcoffee 11.00.8cbe486 (#10130)

* tcoffee 11.00.8cbe486
* Revert meta.yaml
* Update folder name
* add DOI [ci skip]
* Fixing test
* Added t-coffee required runtime deps
* Exclude poa from MacOS build
* Add poa dependency

* Update nglview to v1.1.6 (#10339)

* lumpy: trying to fix skipped build (#10338)

* lumpy: use python version restriction instead of selector

* lumpy: pass on compiler/linker flags to make

* lumpy: add C(PLUS)?_INCLUDE_PATH exports again because the world ain't perfect

* lumpy-sv: also export LIBRARY_PATH...

* lumpy-sv: fix extractSplitReads_BwaMem path

* mac os rebuild (#10347)

* pb-dazzler-0.0.0 (#10348)

* Unblacklist bioperl (#10325)

* fix build

* add missing deps

* update bioperl version

* 3 modules which were moved out of bioperl-run in the latest version

* fix cyclic dep

* move out bio-coordinate + adapt tests everywhere

* unblacklist

* break the (vicious) cycle

* fix tests

* missing dep

* fix versions

* disable temporarily

* disable temporarily

* typos

* fix

* disable this too for now

* disable temp

* good old mac permission problem

* rebuild this one too

* another one

* bump

* bump

* bump

* another one

* bump

* bump

* bump

* bump

* Update vcftools to 0.1.16. (#10345)

* unblacklist (#10349)

* Unblacklist perl-bio-samtools (#10350)

* Unblacklist perl-bio-samtools

* mac perms

* Unblacklist perl-bio-asn1-entrezgene (#10351)

* Unblacklist perl-bioperl-run (#10352)

* increase build number

* updated scvi to v0.1.6 (#10346)

* scvi v0.1.4

* fix pytorch and python version

* fix noarch

* remove fn

* add scvi v0.1.6

* Nglview v1.1.6 (#10343)

* Update nglview to v1.1.6

* remove nglview from blacklist

* Update hyphy to 2.3.14 (#10342)

* Update hyphy to 2.3.14

* disable extended-base

* Create conda_build_config.yaml

* Update meta.yaml

* Update isatools to v0.10.3 (#10340)

* Unblacklist perl-bio-tools-* (#10353)

* Unblacklist perl-bio-tools-*

* trigger new test

* add missing dep

* we need this one on mac

* need this too on mac

* conda is confused between python and perl, it tries to import the module in perl while it's a python one

* mac perm

* t_coffee is too complicated (for me) to isntall on mac

* Update solvebio to v2.6.1 (#10220)

* Unblacklist more bioperl (#10354)

* Unblacklist more bioperl

* fixes + add extutils-makemaker

* remove obsolete checks

* Unblacklist some other perl-bio-* (#10358)

* Unblacklist some other perl-bio-*

* disable for now

* mac perm

* Update bioconda-utils to v0.14.2 (#10360)

* Update bioconda-utils to v0.14.2

* noarch: python

* Update PureCLIP recipe to v1.1.1 (#10361)

* Update beast to v1.10.1 (#10362)

* Add tandem-genotypes (#10286)

* Add tandem-genotypes

* Add tandem-genotypes license

* Add tandem-genotypes noarch

* Add tandem-genotypes host

* Update helperlibs to release-0-1-9 (#10223)

* Update helperlibs to release-0-1-9

* use pip

* Update binsanity to 0.2.6.3 (#10363)

* Update binsanity to 0.2.6.3

* add noarch

* update bioconvert to v0.2.0 (#10316)

* update bioconvert to v0.2.0

* vep: bumped major version (#10366)

* Update treetime to v0.5.0 (#10370)

* new jbrowse release (#10371)

* Unblacklist a few recipes (#10364)

* unblacklist

* lint

* bump

* typo

* force version

* fix augustus 3.2.3

* bump

* bump more

* disable repeatmasker until prl package removed from bioconda

* mac perms

* thanks @bgruening :)

* mac fix

* mac fix

* max fix

* mac fix

* typo

* typo

* trigger new test

* delay repeatmasker

* mac perms

* Fixing some perl (#10375)

* Fix perl-date-manip

* Fix perl-env-path

* Unblacklist

* Fix perl-json-parse

* Unblacklist

* Remove older perl-json-parse

* fix build number

* Rebuild perl-file-slurp (#10376)

* Update mob suite to version 1.4.8 (#10377)

* Add MOB-suite recipe to the channel.MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

* updated recipe to download from URL instead of github

* build python version requirement defined (python >=3.4)

* added build number

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added tests and noarch parameter

* added test statement (import)

* added test statement (import)

* added the new repository and py36 only compile

* made requested corrections by daler. Corrected build number and package string

* Small fixes

* revert deleted row

* New version, fixed sum bugs and improved stability

* Updated 1.4.8 version. The str to int casting issues corrected for the --min... parameters

* new version should reset the build number to 0

* nanopolish out of blacklist (#10368)

* nanopolish outof blacklist

* openmp

* cxx compiler

* config for build

* compiler mess

* skip linting for compilers to accept the hack

* Update meta.yaml

* of course old style needs libgcc

* Dpryan79 fixes 090818 1 (#10378)

* Remove various recipes from the black list

* apoc needs fortran

* skip OSX with agg

* Add bioconductor-zinbwave (#10142)

* Add r-softimpute
* Add bioconductor-zinbwave
* Fixed errors detected during linting
* Added the 'extras' section
* Removed Windows-specific lines from the r-softimpute recipe
* Forgot to remove some Windows-specific lines
* Fixed r-softimpute build.sh
* Fix source url
* Remove r-softimpute
* Add gsl dependency
* Fix gsl version
* skip macOS build

* trigger rebuild

* Remove barrnap, bfc and bgt from the black list (#10380)

* Update snippy to 4.0.0 (#10315)

* Adding a recipe for ksw (#10382)

* Adding a recipe for ksw

* lint?

* use tag as PCK_VERSION

* more

* one commit to rule them all

* cromwell uses find during runtime. With a normal conda installation it can fall back on the host installation, but when running in a biocontainer it only has access to the busybox version which lacks some necessary options. (#10383)

* Perl fix 17 (#10379)

* Fix perl-text-nsp

* Fix perl-image-exiftool

* Fix perl-test-output

* Unblacklist

* Fix shebang

* rebuild flowtools (#10385)

* flowtools

* Update meta.yaml

* skip noarch linting

* Fix typo (#10386)

* Bump perl-vcftools-vcf (#10387)

* Perl parse yapp fix (#10388)

* Bump perl-parse-yapp

* Fix typo

* Enable ensembl-vep from blacklist (#10394)

perl-bioperl now available, pin to updated version to get all
dependencies in sync. Fixes #10366

* Biobb common (#10397)

* First version of biobb_common package recipe

* Adding build noarch section and removing fn section

* Modification in no arch section

* Deleting build.sh

* Ngsplotdb bugfixes (#10396)

* Fix installation for hg19

* Fix hg38

* Fix mm10

* Better syntax

* bioconda release for Trinity v2.8.1

* bioconda updates for v2.8.1
@trstickland

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trstickland Aug 15, 2018

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Please add me as a contributor. Thanks :)

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trstickland commented Aug 15, 2018

Please add me as a contributor. Thanks :)

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Jome0169 Aug 15, 2018

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Hello,

I would like to join the bioconda team and be a contributor. Thank you

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Jome0169 commented Aug 15, 2018

Hello,

I would like to join the bioconda team and be a contributor. Thank you

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cbergman Aug 15, 2018

Hello, I would like to join as a contributor. Thanks!

cbergman commented Aug 15, 2018

Hello, I would like to join as a contributor. Thanks!

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bgruening Aug 16, 2018

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@handetopa, @trstickland, @Jome0169, @cbergman welcome to Bioconda.

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bgruening commented Aug 16, 2018

@handetopa, @trstickland, @Jome0169, @cbergman welcome to Bioconda.

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trstickland Aug 16, 2018

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@bgruening thank you very much

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trstickland commented Aug 16, 2018

@bgruening thank you very much

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aquaskyline Aug 16, 2018

I would like to join as a contributor. Thank you!

aquaskyline commented Aug 16, 2018

I would like to join as a contributor. Thank you!

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cgaray Aug 16, 2018

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Hello, I would like to join as a contributor. Thanks!

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cgaray commented Aug 16, 2018

Hello, I would like to join as a contributor. Thanks!

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matthiasblum Aug 17, 2018

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Following PR #10437 being merged, I'd like to be added to the Bioconda team. Thanks. :)

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matthiasblum commented Aug 17, 2018

Following PR #10437 being merged, I'd like to be added to the Bioconda team. Thanks. :)

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handetopa Aug 17, 2018

Hi, I cannot see myself as a member of the team. Is there anything additional I should still do?

handetopa commented Aug 17, 2018

Hi, I cannot see myself as a member of the team. Is there anything additional I should still do?

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phue Aug 17, 2018

I'd be happy to join in aswell!

phue commented Aug 17, 2018

I'd be happy to join in aswell!

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