Question: Error in loading dependencies due to path length
0
gravatar for thomas.draebing
3 months ago by
Germany
thomas.draebing20 wrote:

Hi,

on our local Galaxy-instance we ran into the following error running MACS2:

/home/galaxy_production/galaxy-dist/database/jobs_directory/001/1752/tool_script.sh: /home/galaxy_production/galaxy-dist/dependency_dir/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/bin/macs2: /home/galaxy_production/galaxy-dist/dependency_dir/_conda/envs/mulled-v1-9745: bad interpreter: No such file or directory

The error is due to the long path of the macs2-dependency, which is longer than 128 chars, which is the maximum length for the shebang used in the macs2 easy install script:

    #!/home/galaxy_production/galaxy-dist/dependency_dir/_conda/envs/mulled-v1-9745eaf08708c75d5cb939b005b2fbbcc13ccefcb86602af9e1bf012d47be274/bin/python
# EASY-INSTALL-SCRIPT: 'MACS2==2.1.1.20160309','macs2'
__requires__ = 'MACS2==2.1.1.20160309'
__import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2')

Although we encountered that error only in MACS2 so far, it could be a general problem, if the conda dependency handler uses long file names for naming the envs. Rolling back to an older version of MACS2 worked for now. Did anybody else encounter this issue? Is there a fix/workaround?

Thanks, Thomas

path admin conda galaxy macs2 • 117 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by thomas.draebing20
1
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Yes, the longer paths are a known Conda limitation https://docs.galaxyproject.org/en/master/admin/conda_faq.html#what-can-i-do-about-this-placehold-error. I just got feedback that Conda needs to be updated manually by the admin right now if already installed. Galaxy release's 17.01 forward that do not have conda installed yet would get/configure the latest default Conda version/config when started up.

I started the conversation with the IUC (tool authors) using the latest MACS2 version of the tool as a reference (https://toolshed.g2.bx.psu.edu/view/iuc/macs2/cb785e26207c).

Please follow and join in with more details if you'd like to: https://gitter.im/galaxy-iuc/iuc?at=5aa6d7db458cbde557279fe5

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k

Sorry for the late reply. Due to some important analyses running on the Galaxy instance, I was only now able to work on the issue. Updating Conda and doing a clean reinstallation of MACS2 and its dependencies solved the issue.

Thanks for the help!

ADD REPLYlink written 3 months ago by thomas.draebing20
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