dmaticzka / bctools Goto Github PK

• update extract_aln_ends.py to handle single mate alignments

fix for multiple jobs: currently temporary files " sortprefix.0000.bam" are created in the calling directory

Currently we are using a slighly modified copy of the official flexbar wrapper: flexbar.pl and flexbar.xml.

This modified version depends on newly created package
Repository package_flexbar_2_5 revision 45d1b8373762 owned by rnateam to allow for automatic installation.

-        <requirement type="binary" version="2.5">flexbar</requirement>
+        <requirement type="package" version="2.5">flexbar</requirement>

At some point, probably after adding flexbar package to main shed, we should propose this to upstream.

It would be a lot easier if this tool would accept BAM files as input directly. Do you mind if I try to implement that?

It would be very nice, if merge_pcr_duplicates would give out the percentage of reads that were discarded in the stdout.

Currently the library splitting workflow creates a lot of files that have to be manually put into the mapping workflow. One possible solution is the use of dataset collections to automate this task.

The following would be the optimal solution for the way the workflows are currently setup:

• multiple paired-end collections as output of workflow
• multiple paired-end collections (plus single fixed input for all) as input for workflow which is then run multiple times

Probably we'll have to start smaller though. What exactly is possible after the last galaxy update?

Since galaxy fails including these dependencies some tools only work when the package is preinstalled on the system. The requested packages are not used

galaxy.tools.deps DEBUG 2015-12-11 09:58:49,829 Building dependency shell command for dependency 'pandas'
galaxy.tools.deps WARNING 2015-12-11 09:58:49,859 Failed to resolve dependency on 'pandas', ignoring

This concerns:

• Repository package_pandas_0_14 revision 045c4645abdf owned by iuc
• Repository package_bedtools_2_19 revision 3ad963111153 owned by iuc requested by Repository package_pybedtools_0_6_6 revision 372c85bed2ca owned by iuc

I have quickly fixed the bedtools dependency by specifically requesting

<repository changeset_revision="e6f4a7398a47" name="package_bedtools_2_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />

, so this may be an issue of the galaxy packages.

tasks:

• switch pandas to package_python_2_7_pandas_0_16
• make extra bedtools dependency independent of testtoolshed
• check if pending update of galaxy pybedtools runs without extra bedtools dependency