Question: Incorrect dependencies used during job run
0
gravatar for rmse17
8 months ago by
rmse170
United States
rmse170 wrote:

Galaxy v17.09 Local install.

After installation of samtools_sort which installed samtools 1.3.1 through Conda, I am seeing unexpected and incorrect behavior when running tools that use samtools where regardless of version specified in the tool dependencies, version 1.3.1 from Conda is always used.

Example: looking at tophat from Devteam, I see tool dependencies listed as following:

Dependency Resolver Details

samtools    0.1.18  Tool_Shed_Package   True    Green checkbox
bowtie  0.12.7  Tool_Shed_Package   True    Green checkbox
tophat  1.4.0   Tool_Shed_Package   True         Green checkvox

Dependencies of this repository

tophat        1.4.0     package     Installed
bowtie        0.12.7    package     Installed
samtools    0.1.18  package     Installed

The tool_dependencies.xml shows the following:


<tool_dependency>
  <package name="bowtie" version="0.12.7">
      <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="&lt;a href=" https:="" toolshed.g2.bx.psu.edu"="" rel="nofollow">https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="0.1.18">
      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="&lt;a href=" https:="" toolshed.g2.bx.psu.edu"="" rel="nofollow">https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="tophat" version="1.4.0">
      <repository changeset_revision="0fea0c8cc6cf" name="package_tophat_1_4_0" owner="devteam" toolshed="&lt;a href=" https:="" toolshed.g2.bx.psu.edu"="" rel="nofollow">https://toolshed.g2.bx.psu.edu" />
    </package>
</tool_dependency>

But when running the tool, I get an error and on the error page saying that I need to use samtools >0.1.17 and I see the following: Job Dependencies

Dependency  Dependency Type     Version
bowtie  galaxy_package  e1c59c194b7b
tophat  galaxy_package  1.4.1
samtools    conda   1.3.1

The log reflects this behavior:

...
galaxy.tools.deps DEBUG 2018-03-30 15:53:28,242 Using dependency bowtie version e1c59c194b7b of type galaxy_package
galaxy.tools.deps DEBUG 2018-03-30 15:53:28,243 Using dependency tophat version 1.4.1 of type galaxy_package
galaxy.tools.deps DEBUG 2018-03-30 15:53:28,243 Using dependency samtools version 1.3.1 of type conda

Similar issue is with other tools that have various versions of samtools specified.

When running bamtools2, the running log is even more interesting, as initially correct version 1.2 is referenced, but then 1.3.1 is used:

galaxy.tools.deps DEBUG 2018-03-30 15:59:21,075 Using dependency bowtie2 version 2.2.6 of type tool_shed_package
galaxy.tools.deps DEBUG 2018-03-30 15:59:21,075 Using dependency samtools version 1.2 of type tool_shed_package
galaxy.jobs.command_factory INFO 2018-03-30 15:59:21,126 Built script [/galaxy/data/jobs/010/10829/tool_script.sh] for tool command [PACKAGE_BASE=/galaxy/dependencies/bowtie2/2.2.6/devteam/bowtie2/a9d4f71dbfb0; export PACKAGE_BASE; . /galaxy/dependencies/bowtie2/2.2.6/devteam/bowtie2/a9d4f71dbfb0/env.sh; PACKAGE_BASE=/galaxy/dependencies/samtools/1.2/devteam/bowtie2/a9d4f71dbfb0; export PACKAGE_BASE; . /galaxy/dependencies/samtools/1.2/devteam/bowtie2/a9d4f71dbfb0/env.sh; bowtie2 --version > /galaxy/data/tmp/GALAXY_VERSION_STRING_34829 2>&1; bowtie2  -p ${GALAXY_SLOTS:-4}  -x /galaxy/data/ce10/bowtie2_index/ce10  -U "/galaxy/data/files/056/dataset_56586.dat"                | samtools view -Su - | samtools sort -o - - > /galaxy/data/files/056/dataset_56608.dat]
galaxy.tools.deps DEBUG 2018-03-30 15:59:21,226 Using dependency samtools version 1.3.1 of type conda

Thanks for your help!

dependency samtools • 349 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by rmse170

cd into one of the job working directories and look at the tool script. It will have a section where it activates the various environments. Run that as the galaxy user, run hash -r and then which samtools. My guess is that for some reason one or more of the conda packages didn't get installed correctly. You'll be able to discern that by see which samtools ends up getting used. If that's the case, you can source activate the appropriate environments and fix them with conda install -c bioconda -c conda-forge whatever the missing packages are.

BTW, don't use tophat unless you need to maintain consistency with a long-running project.

ADD REPLYlink written 8 months ago by Devon Ryan1.9k
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