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galaxyproject / pulsar

Distributed job execution application built for Galaxy
https://pulsar.readthedocs.io
Apache License 2.0
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Tool files are copied without execute bit #341

Open natefoo opened 1 year ago

natefoo commented 1 year ago

Some tools rely on tool files being executable, but when Pulsar transfers them, they are written without the execute bit set, and the tool fails. For example, toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.0:

% ls -l /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/37e1eb05b1b4/text_processing/ansi2html.sh
-rwxr-xr-x. 1 g2main G-803372 11886 Mar  1  2016 /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/37e1eb05b1b4/text_processing/ansi2html.sh*
% ls -l /jetstream2/scratch/main/jobs/53425066/tool_files/ansi2html.sh
-rw-r--r-- 1 g2main G-803372 11886 Nov  3 00:44 /jetstream2/scratch/main/jobs/53425066/tool_files/ansi2html.sh

Which results in the error:

/jetstream2/scratch/main/jobs/53425066/tool_script.sh: line 23: /jetstream2/scratch/main/jobs/53425066/tool_files/ansi2html.sh: Permission denied