Eric Deveaud

Hello, this small modification allows `bwa` to be found based on the user PATH. since python-3.3 `shutil.which()` to provide a cross-platform means of discovering executables. I had to modify the...

problem when -p project dir given as relative location

1

Hello running master branch of ClinSV I noticed that when project dir is given as a relative path it fails with followning error ``` rpm_maker://tmp > clinsv -i /opt/gensoft/tests/datas/ClinSV/NA12878_B37.bam -ref...

master display 0.9 as version info

2

Hello, FIY runnig master branch of ClinSV display version 0.9 and date fromthe past. see: ``` clinsv -h ### This script runs ClinSV on a single node ### Version: 0.9...

Hello, playing with version 1.1.dev I nioticed that commit https://github.com/KCCG/ClinSV/commit/c20c21a3c604c7b484daf6b66223c994dfbc458e seems to have wrong perl shell syntax escaping seems to me that [line ](https://github.com/KCCG/ClinSV/blob/dev-ClinSV-v1.1/clinsv#L476) should be. `print OUT "[ -z...

more processes than available cores

9

Hello using ClinSV-1.0.0 we noticed some potential problem when ClinSV is run through the use of taskset, batch system like slurm, etc... clinsv have some harcoded number of process for...

INSTALL_b38.md :: ClinSV requires python2 AND python3

1

Hello, I noticed in the install from sources documentation, more specifically in install python section. https://github.com/KCCG/ClinSV/blob/master/INSTALL_b38.md#install-python python2 is required clinsv uses python2 for lumpy calls lumpy requires `numpy pysam` python3...

pyrosetta dependency

1

Hello, surely a dump and stupid quesion. ;-) can you point to the URL for pyrosetta (2020.10+release.46415fa) I am not abble to locate it ? is there a strict dependency...

running in a non internet environment

2

Hello, I'm trying to install cellpose-3.0.8 to be run on a cluster whose compute nodes does not have internet access. Installation is done on a ReadOnly shared drive mounted on...