Can't use the most recent version of samtools

[MITiGEM2017]

Running on Ubuntu 14.04. When we use the samtools package from the Ubuntu repository (0.1.19), all tests pass fine. However, if I install the most recent version of samtools (1.5), then the tests fail with the following error:

Sorting BAM file...

• Executing: samtools sort /home/urop/src/MISO/misopy/test-output/sam-output/c2c12.Atp2b1.bam /home/urop/src/MISO/misopy/test-output/sam-output/c2c12.Atp2b1.sorted [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam]

[baileyglen]

I can confirm this. The issue is that samtools sort now requires an explicit -o flag for the output. Going to attempt to fix this.

[martinjvickers]

Yes I can confirm this too.