Installation issues #219

jlfmed · 2013-12-13T20:15:43Z

Hello, thank you for your wonderful work! This looks like the solution we've been looking for for our NGS experiments. Unfortunately, we've been having some issues with installation. It appears to be an issue with brew (which we haven't used before). Could you help us out? Nosudo is used since we do not have root permissions.

Thanks in advance for your help!

Command used: python bcbio_nextgen_install.py /path/to/bcbio-nextgen --tooldir=/path/to/tools --nosudo --isolate

Output:
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew update
Already up-to-date.
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew tap
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew tap homebrew/science
Initialized empty Git repository in /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/Taps/homebrew-science/.git/
remote: Counting objects: 3278, done.
remote: Compressing objects: 100% (2047/2047), done.
remote: Total 3278 (delta 1561), reused 2867 (delta 1210)
Receiving objects: 100% (3278/3278), 706.80 KiB | 354 KiB/s, done.
Resolving deltas: 100% (1561/1561), done.
Tapped 209 formula
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew tap chapmanb/cbl
Initialized empty Git repository in /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/Taps/chapmanb-cbl/.git/
remote: Counting objects: 31, done.
remote: Compressing objects: 100% (22/22), done.
remote: Total 31 (delta 11), reused 27 (delta 9)
Unpacking objects: 100% (31/31), done.
Warning: Could not tap chapmanb/cbl/htslib over homebrew/science/htslib
Warning: Could not tap chapmanb/cbl/samtools over homebrew/science/samtools
Tapped 6 formula
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew tap --repair
Pruned 0 dead formula
Warning: Could not tap chapmanb/cbl/htslib over homebrew/science/htslib
Warning: Could not tap chapmanb/cbl/samtools over homebrew/science/samtools
Tapped 213 formula
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew outdated
[localhost] local: export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && export PERL5LIB=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/lib/perl5:${PERL5LIB} && /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew install --env=inherit cpanminus
==> Downloading https://github.com/miyagawa/cpanminus/archive/1.7102.tar.gz
Already downloaded: /N/u/chobbick/Mason/.cache/Homebrew/cpanminus-1.7102.tar.gz
/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/cpanminus/1.7102: 5 files, 8.0K, built in 2 seconds
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew link --overwrite cpanminus
Warning: Already linked: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/cpanminus/1.7102
To relink: brew unlink cpanminus && brew link cpanminus
[localhost] local: export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && export PERL5LIB=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/lib/perl5:${PERL5LIB} && /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew install --env=inherit expat
==> Downloading http://downloads.sourceforge.net/project/expat/expat/2.1.0/expat-2.1.0.tar.gz
Already downloaded: /N/u/chobbick/Mason/.cache/Homebrew/expat-2.1.0.tar.gz
==> ./configure --prefix=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/expat/2.1.0 --mandir=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/expat/2.1.0/share/man
==> make install
==> Caveats
Note that OS X has Expat 1.5 installed in /usr already.
==> Summary
/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/expat/2.1.0: 11 files, 32K, built in 23 seconds
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew link --overwrite expat
Warning: Already linked: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/expat/2.1.0
To relink: brew unlink expat && brew link expat
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew unlink samtools
Error: No such keg: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/samtools

Fatal error: local() encountered an error (return code 1) while executing '/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew unlink samtools'

Aborting.
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 226, in
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 36, in main
subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/subprocess.py", line 511, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools', '--nosudo', '--isolate', '--data']' returned non-zero exit status 1
chobbick@Mason: /N/dc2/projects/mmgeseq/software/src>

The text was updated successfully, but these errors were encountered:

chapmanb · 2013-12-13T20:32:59Z

Thanks for the report and sorry about the issue. We're currently trying to move to a new version of samtools and bcftools, and it's a bit tricky with dependency issues. I pushed a fix that should address this. If you remove the temporary directory (rm -rf /N/dc2/projects/mmgeseq/software/src/tmpbcbio-install) and then re-run the install command it should pick off where it left off and hopefully finish cleanly.

Thanks for trying bcbio-nextgen out and hope this works for you now.

jlfmed · 2013-12-13T20:34:22Z

Thanks so much for the quick response!

jlfmed · 2013-12-13T22:09:16Z

Looks like a new error --- any advice? Thanks!!

[localhost] local: export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && export PERL5LIB=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/lib/perl5:${PERL5LIB} && /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew install --env=inherit bcftools
==> Installing bcftools dependency: htslib
==> Downloading https://github.com/samtools/htslib/archive/0.2.0-rc5.tar.gz
######################################################################## 100.0%
==> make
==> make install prefix=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/htslib/0.2.0-rc5
ldd: warning: you do not have execution permission for `/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/htslib/0.2.0-rc5/lib/libhts.so.0.0.1'
/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/htslib/0.2.0-rc5: 25 files, 3.1M, built in 14 seconds
==> Installing bcftools
==> Downloading https://github.com/samtools/bcftools/archive/0.2.0-rc5.tar.gz
######################################################################## 100.0%
==> make
gcc -c -g -Wall -Wc++-compat -O2 -I. -I/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/opt/htslib/include kmin.c -o kmin.o
In file included from vcfview.c:5:
bcftools.h:6:21: error: version.h: No such file or directory
make: *** [vcfview.o] Error 1
make: *** Waiting for unfinished jobs....

READ THIS: https://github.com/mxcl/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not mxcl/homebrew):
https://github.com/chapmanb/homebrew-cbl/issues

These open issues may also help:
Homebrew/legacy-homebrew#6333

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && export PERL5LIB=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/lib/perl5:${PERL5LIB} && /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew install --env=inherit bcftools'

Aborting.
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 226, in
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 36, in main
subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/subprocess.py", line 511, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools', '--nosudo', '--isolate', '--data']' returned non-zero exit status 1
chobbick@Mason: /N/dc2/projects/mmgeseq/software/src>

… non-GNU make builds. bcbio/bcbio-nextgen#219

chapmanb · 2013-12-14T11:30:29Z

Thanks for the detailed report. It looks like the Makefile failed to create the version.h file. From reading the Makefile, it appears to have some dependencies on GNU make which might be causing this. What system are you installing on? What does make --version report?

I added a speculative fix that creates the version.h files explicitly, which is helpful anyways since the Makefiles weren't reporting the right version on the command line. Could you try re-running the install and hopefully it'll go cleanly now with this fix.

Sorry again about the issue and thanks for helping work through them.

jlfmed · 2013-12-15T12:53:52Z

No worries about the issue - I just really appreciate your help in trying to work through this (and how on top of these posts you are)!

Here's the output for the make --version:

chobbick@Mason: /N/dc2/projects/mmgeseq/software/src> make -version

GNU Make 3.81

This is free software; see the source for copying conditions.

There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A

PARTICULAR PURPOSE.

This program built for x86_64-redhat-linux-gnu

And unfortunately it's still throwing an error:

copying build/lib.linux-x86_64-2.7/pybedtools/test/data/multibamcov_test.bed -> /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/lib/python2.7/site-packages/pybedtools/test/data

copying build/lib.linux-x86_64-2.7/pybedtools/test/data/small.fastq -> /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/lib/python2.7/site-packages/pybedtools/test/data

copying build/lib.linux-x86_64-2.7/pybedtools/test/data/gdc.50.200.bam -> /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/lib/python2.7/site-packages/pybedtools/test/data

copying build/lib.linux-x86_64-2.7/pybedtools/test/data/b.bed -> /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/lib/python2.7/site-packages/pybedtools/test/data

error: Input/output error

Cleaning up...

Command /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/bin/python -c "import setuptools;file=u'/tmp/pip_build_chobbick/pybedtools/setup.py';exec(compile(open(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-AYSkIZ-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip_build_chobbick/pybedtools

Storing complete log in /N/u/chobbick/Mason/.pip/pip.log

Traceback (most recent call last):

File "bcbio_nextgen_install.py", line 226, in

main(parser.parse_args(), sys.argv[1:])

File "bcbio_nextgen_install.py", line 34, in main

bcbio = bootstrap_bcbionextgen(anaconda, args, remotes)

File "bcbio_nextgen_install.py", line 66, in bootstrap_bcbionextgen

subprocess.check_call([anaconda["pip"], "install", "-r", remotes["requirements"]])

File "/N/soft/rhel6/python/2.7.3/lib/python2.7/subprocess.py", line 511, in check_call

raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command '['/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/bin/pip', 'install', '-r', 'https://raw.github.com/chapmanb/bcbio-nextgen/master/requirements.txt']' returned non-zero exit status -7

chapmanb · 2013-12-15T15:24:09Z

Hmm, I totally don't understand the original error but glad the updated version worked cleanly and got you past that.

This new one looks like you ran into some kind of intermittent disk or network error (error: Input/output error). If you re-run does it fail in the same place? Are you out of space on the install machine? Hopefully a retry here will fix it.

jlfmed · 2013-12-16T02:02:56Z

Thanks again for the help. Unfortunately, there's still an error. It's not a space issue (we still have PBs left).

Here’s the error:
==> Patching
patching file src/api/CMakeLists.txt
==> cmake .. -DCMAKE_INSTALL_PREFIX=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/bamtools/2.3.0 -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFIL
==> make install
/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/bamtools/2.3.0: 26 files, 1.1M, built in 13 seconds
[localhost] local: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew link --overwrite bamtools
Warning: Already linked: /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Cellar/bamtools/2.3.0
To relink: brew unlink bamtools && brew link bamtools
[localhost] local: export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && export PERL5LIB=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/lib/perl5:${PERL5LIB} && /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew install --env=inherit bedtools
==> Downloading https://github.com/arq5x/bedtools2/archive/v2.18.0.tar.gz
Already downloaded: /N/u/chobbick/Mason/.cache/Homebrew/bedtools-2.18.0.tar.gz
==> make
obj/InputStreamMgr.o: In function InputStreamMgr::detectBamOrBgzip(int&, int)': InputStreamMgr.cpp:(.text+0x89e): undefined reference toBamTools::BamReader::OpenStream(std::basic_istream<char, std::char_traits >)'
InputStreamMgr.cpp:(.text+0x9a7): undefined reference to `BamTools::Internal::BgzfStream::OpenStream(std::basic_istream<char, std::char_traits >, BamTools::IBamIODevice::OpenMode)'
collect2: ld returned 1 exit status
make: *** [all] Error 1

READ THIS: https://github.com/mxcl/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not mxcl/homebrew):
https://github.com/homebrew/homebrew-science/issues

/N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:353:in open_http': 404 Not Found (OpenURI::HTTPError) from /N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:708:inbuffer_open'
from /N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:210:in block in open_loop' from /N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:208:incatch'
from /N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:208:in open_loop' from /N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:149:inopen_uri'
from /N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:688:in open' from /N/dc2/projects/mmgeseq/software/src/ruby/lib/ruby/2.0.0/open-uri.rb:30:inopen'
from /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/Homebrew/utils.rb:265:in open' from /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/Homebrew/utils.rb:282:ineach_issue_matching'
from /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/Homebrew/utils.rb:294:in issues_for_formula' from /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/Homebrew/exceptions.rb:178:inissues'
from /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/Homebrew/exceptions.rb:212:in dump' from /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/brew.rb:118:inrescue in

'
from /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/Library/brew.rb:58:in `'

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-which gcc} && export CXX=${CXX:-which g++} && export PERL5LIB=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/lib/perl5:${PERL5LIB} && /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/brew install --env=inherit bedtools'

Aborting.
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 226, in
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 36, in main
subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/subprocess.py", line 511, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools', '--nosudo', '--isolate', '--data']' returned non-zero exit status 1

This program built for x86_64-redhat-linux-gnu

…5x/bedtools2#3). bcbio/bcbio-nextgen#220 bcbio/bcbio-nextgen#219

chapmanb · 2013-12-16T03:27:32Z

Sorry about the continued problems. This looks like a build error in bedtools. I pushed a fix and provided more information in this thread: #220 (comment). Hope an update will clean this up for you. Thanks again.

jlfmed · 2013-12-16T16:30:37Z

Thanks so much for sticking through this with us! We finally got a successful installation, but we're having difficulties upgrading dependencies. The original command and output is below:

jllin@Mason: /N/dc2/projects/mmgeseq/bcbio_test/project1/work> bcbio_nextgen.py ../config/project1.yaml
[2013-12-16 11:12] Using input YAML configuration: /N/dc2/projects/mmgeseq/bcbio_test/project1/config/project1.yaml
[2013-12-16 11:12] Checking sample YAML configuration: /N/dc2/projects/mmgeseq/bcbio_test/project1/config/project1.yaml
[2013-12-16 11:12] Preparing 1_131216_project1
[2013-12-16 11:12] Preparing 2_131216_project1
[2013-12-16 11:13] Testing minimum versions of installed programs
Traceback (most recent call last):
File "/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/bcbio_nextgen.py", line 54, in
main(**kwargs)
File "/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/tools/bin/bcbio_nextgen.py", line 38, in main
run_main(**kwargs)
File "/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 44, in run_main
fc_dir, run_info_yaml)
File "/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
versioncheck.testall(pipeline_items)
File "/N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/versioncheck.py", line 60, in testall
"\n".join(msgs))
OSError: Program problems found. You can upgrade dependencies with:
bcbio_nextgen.py upgrade -u skip --tooldir=/usr/local

Installed version of samtools sort does not have support for multithreading (-@ option) required to support bwa piped alignment and BAM merging. Please upgrade to the latest version from http://samtools.sourceforge.net/
java version 1.7 or better required for running GATK and other tools. Found version at /N/dc2/projects/mmgeseq/software/src/jre1.7.0_25/bin/java

And the output from trying to upgrade the dependencies is here:

chobbick@Mason: /N/dc2/projects/mmgeseq/software/src> python bcbio_nextgen_install.py upgrade -u stable --nosudo --tools --data
usage: bcbio_nextgen_install.py [-h] [--tooldir TOOLDIR]
[--toolplus {protected,data}]
[--genomes GENOMES] [--aligners ALIGNERS]
[--nodata] [--nosudo] [--isolate]
[-u {stable,development}]
[--tooldist {minimal,full}]
[--distribution {ubuntu,debian,centos,scientificlinux,macosx}]
datadir
bcbio_nextgen_install.py: error: unrecognized arguments: --tools --data

Any more tips for us? Sorry again for having all this back and forth!

chapmanb · 2013-12-16T20:51:27Z

Awesome to hear you got an initial install done. Thanks for the persistence. It looks like there are a couple of issues:

The samtools error indicates that you've got an older version of samtools on your PATH. Adding /N/dc2/projects/mmgeseq/software/src/bcbio-nextgen/bin to the front of your PATH should fix that and pick up the one installed by bcbio_nextgen.
The --tools and --data arguments are new in version 0.7.5. Is it possible you installed an older version (or have one in your PATH?). If so, you can update to the latest release with bcbio_nextgen.py upgrade -u stable and then you should be able to use the --tools and --data arguments for upgrading those. Sorry for the confusion, this changed to try and make the options more stable and not accidentally upgrade things when not intended.

Hope these get you working smoothly with an initial run. Thanks again,
Brad

jlfmed · 2013-12-17T14:48:00Z

Thanks Brad, the PATH switch helped with samtools --- it was pulling from a previously installed version as you suggested. We're still having trouble with the --tools and --data arguments though. How can you tell which version you have? If you use --version, it says 0.7.5. We only have one version of bcbio_nextgen installed.

jllin@Mason: /N/dc2/projects/mmgeseq/bcbio_test/project1/work> bcbio_nextgen.py --version
0.7.5

Thanks again for your help!

jlfmed · 2013-12-17T16:54:16Z

Hi Brad, sorry for the extra post, but I think we got it figured out! Thanks so much!

chapmanb · 2013-12-17T18:01:38Z

That's the kind of comment I like. Great job. Nice to hear things are working.

chapmanb closed this as completed in chapmanb/cloudbiolinux@c4fb5e4 Dec 13, 2013

chapmanb added a commit to chapmanb/homebrew-cbl that referenced this issue Dec 14, 2013

Explicitly define bcftools and samtools versions to avoid issues with…

22909cd

… non-GNU make builds. bcbio/bcbio-nextgen#219

chapmanb mentioned this issue Dec 16, 2013

Build error on CentOS/RedHat systems with 2.18.0 arq5x/bedtools2#3

Closed

chapmanb added a commit to chapmanb/cloudbiolinux that referenced this issue Dec 16, 2013

Pin bedtools to previous version to avoid build errors on 2.18.0 (arq…

4072d40

…5x/bedtools2#3). bcbio/bcbio-nextgen#220 bcbio/bcbio-nextgen#219

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Installation issues #219

Installation issues #219

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jlfmed commented Dec 16, 2013

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jlfmed commented Dec 16, 2013

chapmanb commented Dec 16, 2013

jlfmed commented Dec 17, 2013

jlfmed commented Dec 17, 2013

chapmanb commented Dec 17, 2013