galaxyproject / galaxyproject/usegalaxy-tools

Fix dependency for cshl_fastx_barcode_splitter 1.0.1 at org

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Description

tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.1

fails at `org`, Ok at `eu`

test histories:
* https://usegalaxy.org/u/jen/h/test-cshlfastxbarcodesplitter-101
* https://usegalaxy.eu/u/jenj/h/test-cshlfastxbarcodesplitter-101

tool tests (all pass, doesn't include a `bz2` test): https://github.com/mvdbeek/usegalaxy-tests/issues/50

Cannot uncompress `bz2`. Uncompressed or `gz` work fine.

> /corral4/main/jobs/044/621/44621152/tool_script.sh: line 22: bzcat: command not found
> Use of uninitialized value $first_char in ord at /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/015dc921d814/fastx_barcode_splitter/fastx_barcode_splitter.pl line 383.
> Use of uninitialized value $first_char in string eq at /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/015dc921d814/fastx_barcode_splitter/fastx_barcode_splitter.pl line 385.
> Use of uninitialized value $first_char in string eq at /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/015dc921d814/fastx_barcode_splitter/fastx_barcode_splitter.pl line 389.
> Use of uninitialized value $first_char in concatenation (.) or string at /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/015dc921d814/fastx_barcode_splitter/fastx_barcode_splitter.pl line 394.
> Error: unknown file format. First character = '' (expecting > or @)

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with the cshl_fastx_barcode_splitter 1.0.1 tool identified by the tool_id and inspect how its bz2 dependency is declared. Reproduce the failure using the linked org test history, compare with the working eu history, and verify that bz2 input completes successfully on org without the bzcat error.

Written by the indexing model from the issue text.

Assessment

Tech stack
shell
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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