Release of GenPipes 4.3.1

[edouard.henrion]

A new release of the GenPipes, 4.3.1 is now available.

 

What's new? 

==========

This release is mainly a bug-fix release :

* Tumor Pair : ensures errors are detected for bwa_mem_sort_sam

* MethylSeq : debugged filter_snp_cpg

* Nanopre CoVSeq : fixed GPU_QUEUE bug

Features : 

* MethylSeq : differential expression analysis added back to the pipeline

* All pipelines : added timestamp and command used in the configuration trace file
 

Where to find it?

============ 

* This version tarball is in bitbucket : 

https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.3.1.tar.gz

 

* The module mugqic/genpipes/4.3.1 is installed on Abacus (MGC), Béluga, Graham, Cedar and Narval Compute Canada clusters.

 

* The source code is in bitbucket :

https://bitbucket.org/mugqic/genpipes

 

* For more documentation, please refer to :
https://genpipes.readthedocs.io/

 

Where is the detailed ChangeLog? 

========================== 

A ChangeLog (CHANGELOG.md) is available in the archive as well as in the repository.

 

Since we use git, there are many ways to get the details in many formats. 

One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert, 

which lists the commits by tag and author: 

https://raw.github.com/sebhtml/ray/master/scripts/dump-ChangeLog.sh 

[Shraddha Pai]

Hi,

I would like to run GenPipes on a Compute Canada server but cannot find any mugqic modules on Graham.

I'm logged into the Graham login node graham.computecanada.ca.

Neither "module avail" nor "module spider mugqic*" turns up anything.

Can you please advise?

Thanks,Shraddha

--

Shraddha Pai
Principal Investigator, OICR, Toronto
Assistant Professor, University of Toronto

[Édouard Henrion]

Hi Shraddha,

Thanks for your interest in GenPipes.

First know that we have documentation available here.

Before you can use our pipelines on Graham (or any other Compute Canada server), you have to make sure our modules are available in your environment.

You can achieve this with the following command : 

  module use /cvmfs/soft.mugqic/root/modulefiles

But I recommend you add this into your .bash_profile or .bashrc, so it's done automatically each time you log in.

You could go with the following (more details here) :

  ## MUGQIC genomes and modules

  export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/root

  module use $MUGQIC_INSTALL_HOME/modulefiles

Regards,

Edouard

[Shraddha Pai]

Hi Edouard,

Great, I see it now. Thank you also for the documentation website. 

I will follow the instructions to set up a WGBS analysis pipeline and will post in a separate thread if there are any roadblocks.

Thanks again for replying so promptly,

Shraddha