Add python version option to planemo test command #2485
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This changeset: - upgrades the STAR tool and the associated data manager to the latest version of STAR - restructures the tool interface in an attempt to present important parameters first - introduces a new versioned index data table, which is used to offer only version-compatible indexes in the tool interface - adds the necessary files for testing the use of cached indexes STARsolo parameters will have to be added separately, or be introduced through a dedicated tool.
Also fixes setting metadata on output datasets and edge cases with enabling/disabling chimeric alignments.
For readability, also start distinguishing between with-gtf and with-gene-model parameters and variables.
Flattens the algorithmic parameter section partially, documents the exact recommendations for using the tool upstream of STAR-Fusion, and switches the default for unmapped reads to be retained in the BAM output (since that's the setting recommended for STAR-Fusion, and because they are easy to eliminate, but impossible to add later.
Bandage: add parameters to add name and length labels to nodes
Expect to fail: bowtie2 won't run under python3. Fix to be added in subsequent commit.
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Travis fails at the lint stage (i.e. before actual testing) because several Python files are not Python3-compatible. |
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@nsoranzo got it! (i saw it failed as expected, but for the wrong reason). I'll get to this later today. |
Diffbind: update to v2.10.0 and fix some warnings
Added quotes to names of snippy output dirs for snippy-core
STAR wrapper update
update jbrowse to 1.16.5
…xyproject#2463) Changed the TBprofiler wrapper target version 2.1.0 to version 2.4
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Can you please rebase the pull request? Unfortunately we had to do a force-push on the master branch. Please let us know if you have issues and we can do it for you. |
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@nsoranzo yep, i'm on it. |
Also, change python version to 3.6. This is the first step in ref to: galaxyproject#2168
Expect to fail: bowtie2 won't run under python3. Fix to be added in subsequent commit.
Done mostly using 2to3 with manual sanity checks. Add `from __future__ import print_function` where converting print to print(). This only covers files that had linting errors.
5 tasks
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This has been replaced by #2493 |
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Also, change python version to 3.6.
This is the first step in ref to:
#2168
Ping @mvdbeek
FOR CONTRIBUTOR: