setup.sh fails on legacy bam-to-json.pl due to samtools update #501

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cmdcolin opened this Issue Aug 18, 2014 · 10 comments

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cmdcolin commented Aug 18, 2014

Currently setup.sh is coded to checkout the master branch from the samtools github to support Bio::SamTools. However, samtools was recently updated to version 1.0, and it now has a new dependency on htslib, so the build fails.

Therefore we get errors such as

$ ./setup.sh 
...
Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... failed.  See setup.log file for error messages. If you really need bam-to-json.pl (most users don't), try reading the Bio-SamTools troubleshooting guide at https://metacpan.org/source/LDS/Bio-SamTools-1.33/README for help getting Bio::DB::Sam installed.

And in setup.log users will see

...
+ rm samtools-master.zip
+ perl -i -pe 's/^CFLAGS=\s*/CFLAGS=-fPIC / unless /\b-fPIC\b/' samtools-master/Makefile
+ make -C samtools-master -j3 lib
Makefile:85: ../htslib/htslib.mk: No such file or directory
make: *** No rule to make target `../htslib/htslib.mk'.  

bam-to-json is a legacy feature, but this issue will affect all users running setup.sh on a fresh installation

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cmdcolin Aug 18, 2014

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I would recommend switching from downloading the master branch to using https://github.com/samtools/samtools/releases/tag/0.1.20 which is the final version of samtools without htslib. In the future, there could be more interesting things added to samtools, but this version seems stable. Note: This change would not affect the use of typical alignments tracks tracks since that is all done within javascript, it only effects legacy tracks

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cmdcolin commented Aug 18, 2014

I would recommend switching from downloading the master branch to using https://github.com/samtools/samtools/releases/tag/0.1.20 which is the final version of samtools without htslib. In the future, there could be more interesting things added to samtools, but this version seems stable. Note: This change would not affect the use of typical alignments tracks tracks since that is all done within javascript, it only effects legacy tracks

@cmdcolin cmdcolin closed this in 612e983 Aug 20, 2014

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CikLa Nov 20, 2014

Hi,
I am new in this. My setup.sh stucked when here:

"Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ..."

I have upgrade my Samtools into version 0.1.20 but still cannot solved this. Any suggestion on how to solve this?

CikLa commented Nov 20, 2014

Hi,
I am new in this. My setup.sh stucked when here:

"Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ..."

I have upgrade my Samtools into version 0.1.20 but still cannot solved this. Any suggestion on how to solve this?

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cmdcolin Nov 20, 2014

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Most users don't require the legacy feature support (most users use the add-bam-track.pl instead of bam-to-json.pl script)

If you're interested though, can you paste the output of setup.log?

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cmdcolin commented Nov 20, 2014

Most users don't require the legacy feature support (most users use the add-bam-track.pl instead of bam-to-json.pl script)

If you're interested though, can you paste the output of setup.log?

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CikLa Nov 21, 2014

I attach the setup.log here.

May I know, how to use the add-bam-track.pl instead of bam-to-json.pl
script?

On Fri, Nov 21, 2014 at 1:58 AM, Colin Diesh notifications@github.com
wrote:

Most users don't require the legacy feature support (most users use the
add-bam-track.pl instead of bam-to-json.pl script)

If you're interested though, can you paste the output of setup.log?

Reply to this email directly or view it on GitHub
#501 (comment).

CikLa commented Nov 21, 2014

I attach the setup.log here.

May I know, how to use the add-bam-track.pl instead of bam-to-json.pl
script?

On Fri, Nov 21, 2014 at 1:58 AM, Colin Diesh notifications@github.com
wrote:

Most users don't require the legacy feature support (most users use the
add-bam-track.pl instead of bam-to-json.pl script)

If you're interested though, can you paste the output of setup.log?

Reply to this email directly or view it on GitHub
#501 (comment).

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the most basic usage for add-bam-track.pl is this:

  1. copy your bam file and bai file into the data directory
  2. run "add-bam-track.pl --bam_url yourfile.bam --label bam_track"

this will update your trackList.json with the bam track info. Note: the "bam_url" argument is a URL path that is relative to the data directory, that's why I recommend just moving the BAM file into the data directory.

also I didn't get your setup.log, I guess it didn't accept the attachment

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cmdcolin commented Nov 21, 2014

the most basic usage for add-bam-track.pl is this:

  1. copy your bam file and bai file into the data directory
  2. run "add-bam-track.pl --bam_url yourfile.bam --label bam_track"

this will update your trackList.json with the bam track info. Note: the "bam_url" argument is a URL path that is relative to the data directory, that's why I recommend just moving the BAM file into the data directory.

also I didn't get your setup.log, I guess it didn't accept the attachment

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CikLa Nov 21, 2014

Here I paste the setup.log. Sorry I am a new newbie in this.
==removed==

CikLa commented Nov 21, 2014

Here I paste the setup.log. Sorry I am a new newbie in this.
==removed==

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Unfortunately this looks incomplete. I dunno if github just didn't allow you to paste that much or what, but perhaps a pastebin.com site would help.

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cmdcolin commented Nov 21, 2014

Unfortunately this looks incomplete. I dunno if github just didn't allow you to paste that much or what, but perhaps a pastebin.com site would help.

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CikLa Nov 21, 2014

Sorry, the email truncated the setup.log. I have put it here:
http://pastebin.com/S9Z80rA5
On 21 Nov 2014 23:52, "Colin Diesh" notifications@github.com wrote:

Unfortunately this looks incomplete. I dunno if github just didn't allow
you to paste that much or what, but perhaps a pastebin.com site would
help.

Reply to this email directly or view it on GitHub
#501 (comment).

CikLa commented Nov 21, 2014

Sorry, the email truncated the setup.log. I have put it here:
http://pastebin.com/S9Z80rA5
On 21 Nov 2014 23:52, "Colin Diesh" notifications@github.com wrote:

Unfortunately this looks incomplete. I dunno if github just didn't allow
you to paste that much or what, but perhaps a pastebin.com site would
help.

Reply to this email directly or view it on GitHub
#501 (comment).

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cmdcolin Nov 21, 2014

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It appears there is already an existing version of bioperl installed to the system and it might be creating a conflict. This version you have I think is 1.6.0. If possible, I might remove that one and let jbrowse install the upgrade

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cmdcolin commented Nov 21, 2014

It appears there is already an existing version of bioperl installed to the system and it might be creating a conflict. This version you have I think is 1.6.0. If possible, I might remove that one and let jbrowse install the upgrade

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CikLa Nov 23, 2014

Thanks a lot, the problem has been solved. I removed the BioPerl before run
the setup.sh. Really appreciate. Thanks!

On Sat, Nov 22, 2014 at 12:38 AM, Colin Diesh notifications@github.com
wrote:

It appears there is already an existing version of bioperl installed to
the system and it might be creating a conflict. This version you have I
think is 1.6.0. If possible, I might remove that one and let jbrowse
install the upgrade

Reply to this email directly or view it on GitHub
#501 (comment).

CikLa commented Nov 23, 2014

Thanks a lot, the problem has been solved. I removed the BioPerl before run
the setup.sh. Really appreciate. Thanks!

On Sat, Nov 22, 2014 at 12:38 AM, Colin Diesh notifications@github.com
wrote:

It appears there is already an existing version of bioperl installed to
the system and it might be creating a conflict. This version you have I
think is 1.6.0. If possible, I might remove that one and let jbrowse
install the upgrade

Reply to this email directly or view it on GitHub
#501 (comment).

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