Lance Parsons
lparsons

Jul 28, 2016
@lparsons
History item being viewed is not marked when it's part of a collection
lparsons deleted branch trinity_fix at lparsons/tools-iuc
Jul 13, 2016
Jul 12, 2016
@lparsons
r_3.2.1_linux_x64.tar.gz from depot seems to be missing libblas.a , libblas.so and libblas.so.3
Jul 12, 2016
lparsons commented on pull request galaxyproject/tools-iuc#879
@lparsons

@abretaud Thanks for the merge and toolshed update. Can you reset the metadata on the toolshed? It seems if you don't do that, the tool version lin…

Jul 12, 2016
@lparsons

@abretaud I just know that things fail if I use the tarball at https://depot.galaxyproject.org/software/r/r_3.2.1_linux_x64.tar.gz. If I build R us…

Jul 12, 2016
@lparsons
Set max_ins_size only in paired-end mode
1 commit with 2 additions and 2 deletions
Jul 12, 2016
Jul 12, 2016
@lparsons
Building express fails: library not found for -lprotobuf
Jul 11, 2016
@lparsons

From my testing, it looks like no changes are needed to the tool_dependency.xml file for any of the tools (package_r_3_2_1, package_bioconductor_ed…

Jul 11, 2016
@lparsons

@davebx Is this something you can help with?

Jul 11, 2016
@lparsons

@abretaud Looks like this is indeed an issue with the R package. I was able to get things working by adding the atlas package to set_environment_fo…

Jul 11, 2016
@lparsons

Just noticed that R is actually not built on my system (64-bit Linux), but instead a pre-compiled binary is downloaded from galaxydepot. I'll see i…

Jul 11, 2016
@lparsons

I was able to set the ATLAS environment for deseq2 and edger, but the same error occurred. I also added it to R, but none of these things fixed the…

Jul 11, 2016
@lparsons

@abretaud I'm not sure either. I'm trying to test adding it to deseq2 now, but I haven't been able to generate a valid set_environment_for_install

Jul 11, 2016
@lparsons

@abretaud Thanks for helping with the other issues, and sorry to bug you, but I thought you might be able to shed some light on this... One possibl…

lparsons deleted branch package_trinity_2_1_1_fix at lparsons/tools-iuc
Jul 11, 2016
Jul 8, 2016
@lparsons
package_deseq2_1_10_0 and package_bioconductor_edger_3_14_0 fail to install - /usr/bin/ld: cannot find -lblas
Jul 8, 2016
@lparsons
Avoid compiling trinity's packaged samtools
1 commit with 1 addition and 0 deletions
Jul 8, 2016
Jul 8, 2016
@lparsons
  • @Slugger70 beb0a0e
    JBrowse: Added option to use locally cached genomes as reference fast…
  • @lparsons 31df7a6
    Set zlib environment for install of fontconfig (#830)
  • 23 more commits »
Jul 8, 2016
@lparsons

Hmmm... Actually, looking at this now, it's not clear that package_trinity_2_1_1 ever actually uses the built samtools 0.1.19. There is no directiv…

Jul 8, 2016
@lparsons

A bit more digging and it seems like having C_INCLUDE_PATH and CPLUS_INCLUDE_PATH pointing to zlib 1.2.8 is causing the issue. If I unset those, sa…

Jul 7, 2016
@lparsons

That's for the pointers @abretaud. I didn't get to look at it much, but I did confirm the problem comes from sourcing env.sh from the zlib package.…

Jul 7, 2016
@lparsons

@abretaud Just wondering if you've made any progress on this before I start looking into it myself.

Jul 5, 2016
lparsons commented on pull request galaxyproject/tools-iuc#830
@lparsons

@bgruening No problem, I know you guys were at GCC. Hope it all went well. Besides, I'm now actually held up by #836.

Jun 30, 2016
lparsons commented on pull request galaxyproject/tools-iuc#845
@lparsons

@bgruening I had thought to try to preserve history (and I thought this would have worked, so no big deal). But if it's a pain, preservation of his…

Jun 27, 2016
lparsons commented on pull request galaxyproject/tools-iuc#845
@lparsons

I've attempted to merge htseq-count with my fork of the IUC tools, but it seems Github won't let me create a Pull Request: There isn’t anything to …

Jun 27, 2016
Jun 27, 2016
@lparsons
Jun 27, 2016
lparsons commented on pull request galaxyproject/tools-iuc#845
@lparsons

@dpryan79 Waiting for this to be pushed to main toolshed before I push the updated htseq_count package. Also, I'll submit a PR to merge this in the…