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cgat-developers / cgat-apps

cgat-apps repository
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travis tests are failing and it seems on local testing on mac that ch… #56

Closed Acribbs closed 4 years ago

Acribbs commented 4 years ago

…anging pysam to 0.15.2 makes bam2bam work

Acribbs commented 4 years ago

@sebastian-luna-valero Travis tests are failing now and im not sure why. In our previous travis test in october ran to completion. Forcing Travis to re-run tests on the master seems to make it fail. On local testing on my mac, when I downregulate pysam from 0.15.3 to 0.15.2 bam2bam script works, while it originally failed for the following reason:

from cgat.BamTools.bamtools import bam2bam_filter_bam, SetNH
  File "libcalignedsegment.pxd", line 66, in init cgat.BamTools.bamtools
ValueError: pysam.libcalignedsegment.PileupColumn has the wrong size, try recompiling. Expected 88, got 72

Not sure if this is the reason for the tests failing on travis (I installed cgat-apps using conda, while our install script picks up the git branch) but I have pinned the version of pysam to see if it makes a difference.

Do you have any suggestions?

Acribbs commented 4 years ago

ok, well that failed to do anything

sebastian-luna-valero commented 4 years ago

Well, you're right; updating pysam from 0.15.2 to 0.15.3 makes the following tests fail:

cat /home/travis/build/cgat-developers/cgat-apps/tests/bam2bam.py/sample_gsnap.bam | cgat bam2bam -v 0 --log=/dev/null --method=filter --filter-method=NM --reference-bam-file=/home/travis/build/cgat-developers/cgat-apps/tests/bam2bam.py/sample_star.bam


* bam2stats.py:

cat /home/travis/build/cgat-developers/cgat-apps/tests/bam2stats.py/paired.bam | cgat bam2stats --force-output

cat /home/travis/build/cgat-developers/cgat-apps/tests/bam2stats.py/paired.bam | cgat bam2stats --output-details --fastq-file=/home/travis/build/cgat-developers/cgat-apps/tests/bam2stats.py/paired.fastq.1.gz --force-output


Do you know why?

Best regards,
Sebastian
Acribbs commented 4 years ago

I think there may have been something wrong with the build on 0.15.3. See this https://github.com/pysam-developers/pysam/pull/814

Acribbs commented 4 years ago

@sebastian-luna-valero I think we leave pysam pinned to 0.15.2 for the time being, until pysam has sorted it automatic pypi issues. Sorry, just seen that you have merged cgatcore too. Will merge this too, if you dont agree please revert