Problem running runMantaWorkflowDemo

[tillea]

I'm a member of the Debian Med team which is a group inside Debian with the objective to package free software in life sciences and medicine for official Debian. So I intended to include manta into Debian and have tried some packaging attempt. I need to confess that I patched the build system to use zlib, htslib, samtools and pyflow to use the Debian packaged version. The issue described below is happening with manta release tag 1.1.0 and seems to be related to pyflow. I made sure that the Debian version is 1.1.4 as specified inside the cmake check. (I noticed that manta 1.0.2 was checking for pyflow 1.1.2.) When running runMantaWorkflowDemo.py to verify whether manta works as expected I'm running into

 [ERROR] AttributeError: 'WorkflowOptions' object has no attribute 'minCandidateVariantSize'

I've attached the full log created by this script.
Any idea what might went wrong?
Kind regards, Andreas.

[ctsa]

Thank you for working to package Manta for Debian. I understand that the default manta build design is inclined towards vendoring many of our dependencies, which is going to make this process harder -- we'd like to improve the situation with more flexible options in the build system. If you can expose your build edits on a branch/fork somewhere we might be able to discuss what can developed into new build options.

Regarding the immediate issue:

• Manta requires an ini file to provide some of its default paramaters. The default version is: https://github.com/Illumina/manta/blob/master/src/python/bin/configManta.py.ini
• The ini file is searched for by default in the same directory as configManta.py
• The error above seems to be the result of a missing ini file (I recreated the error locally). I thought we were issuing a much more direct error message about a missing ini file at config time, but your experience highlights that this is not being handled well at the moment, I have ticketed this as a bug: Manta must issue an error message when no ini file is found #79

[tillea]

Hi Chris, thanks for the quick reply.

On Wed, May 03, 2017 at 12:10:21PM -0700, Chris Saunders wrote: Thank you for working to package Manta for Debian. I understand that the default manta build design is inclined towards vendoring many of our dependencies, which is going to make this process harder -- we'd like to improve the situation with more flexible options in the build system. If you can expose your build edits on a branch/fork somewhere we might be able to discuss what can developed into new build options.

The packaging is available in our packaging Git and here is the deep link to all patches I'm currently applying: https://anonscm.debian.org/cgit/debian-med/manta.git/tree/debian/patches I intended to send a link once the package is fully finished but since we now have contact here they are. One specific one is fix_comparison.patch - you probably want to apply something like this in your code since recent gcc versions will fail otherwise when strict options are set.

Regarding the immediate issue: * Manta requires an ini file to provide some of its default paramaters. The default version is: https://github.com/Illumina/manta/blob/master/src/python/bin/configManta.py.ini * The ini file is searched for by default in the same directory as `configManta.py` * The error above seems to be the result of a missing ini file (I recreated the error locally). I thought we were issuing a much more direct error message about a missing ini file at config time, but your experience highlights that this is not being handled well at the moment, I have ticketed this as a bug: #79

Thanks, I'll check this tomorrow.

[tillea]

Hi again,

On Wed, May 03, 2017 at 12:10:21PM -0700, Chris Saunders wrote: * Manta requires an ini file to provide some of its default paramaters. The default version is: https://github.com/Illumina/manta/blob/master/src/python/bin/configManta.py.ini * The ini file is searched for by default in the same directory as `configManta.py`

The current packaging installs: $ ls -l /usr/share/manta/configManta.py* -rwxr-xr-x 1 root root 6988 Nov 15 14:29 /usr/share/manta/configManta.py -rw-r--r-- 1 root root 5956 Mai 4 17:02 /usr/share/manta/configManta.pyc lrwxrwxrwx 1 root root 26 Nov 15 14:29 /usr/share/manta/configManta.py.ini -> /etc/manta/configManta.ini In Debian configuration belongs to /etc thus the symlink. The ini file is unchanged and contains minCandidateVariantSize: $ grep minCandidateVariantSize /usr/share/manta/configManta.py.ini minCandidateVariantSize = 8

* The error above seems to be the result of a missing ini file (I recreated the error locally). I thought we were issuing a much more direct error message about a missing ini file at config time, but your experience highlights that this is not being handled well at the moment, I have ticketed this as a bug: #79

Unfortunately the error remains despite I have added the said link. Do you have any further hints? Kind regards, Andreas. PS: regarding my remark about the fix_comparison.patch: It is only needed when using htslib >= 1.4.

[ctsa]

It looks like you've patched the code to look for the ini file in /etc/manta, but the code which installs the ini file to the bin directory here:

https://github.com/Illumina/manta/blob/master/src/python/bin/CMakeLists.txt#L33

...is unchanged (or I missed that in your patches?)

[tillea]

On Mon, May 15, 2017 at 10:27:23AM -0700, Chris Saunders wrote: It looks like you've patched the code to look for the ini file in /etc/manta, but the code which installs the ini file to the bin directory here: https://github.com/Illumina/manta/blob/master/src/python/bin/CMakeLists.txt#L33 ...is unchanged (or I missed that in your patches?)

I manually moved the ini file right into place inside debian/rules file https://anonscm.debian.org/cgit/debian-med/manta.git/tree/debian/rules#31 So the ini file exists: $ ls /usr/share/manta/*.ini /etc/manta /usr/share/manta/configManta.py.ini /etc/manta: configManta.ini $ readlink /usr/share/manta/*.ini /etc/manta/configManta.ini So there is no real need to tweak the said CMakeLists.txt if I'm not totally wrong. Thanks for the hint anyway - may be you come up with some further things I could try.