The command line tools PE_fragment_size and bigwigCompare not part of galaxy. about deeptools HOT 9 CLOSED

bigwigCompare has already a wrapper but if I remember correctly the tools was not stable enough. Is that still true @friedue ?

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yes, it is true. they are untested, therefore they should not be added to the major release within the next two weeks, but we should start testing and incorporating them eventually.

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One issue related to deepTools use of bigwig is the lack of support from the bx-python API to report the chromosome names and lengths. bigwigCompare uses parses the command line output of USCS/bigWigInfo to get such data, and in heatmapper we just guess if by adding of removing 'chr', a chromosome name match is found.

There are two alternatives for this. One is to use another bigWig library. There is one that directly uses the bigwig .c routines from the original ucsc implementation: http://tsznxx.appspot.com/BigWigFile

We may ask the author if we could include this into deepTools. I think this could should be much faster but testing is needed. In the source code I noticed that you can query the chromosome names.

The other option is to change the behaviour of bx-python. I have looked at the source code and the functions to query the chromosome names are present but not public. So, with minimal changes this feature can be activated.

The problem is that this will require a very recent version of bx-python for deepTools installation and I don't know if this may affect galaxy installations.

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It will probably not effect the galaxy installation, as we can depend on any version, independent from Galaxy.

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bamCompare is not included in the testtoolshed, is PE_fragment_size also ready to ship?

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I think we should add it to the toolshed.

On Thu, Sep 4, 2014 at 3:16 PM, Björn Grüning [email protected]
wrote:

bamCompare is not included in the testtoolshed, is PE_fragment_size also
ready to ship?

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#45 (comment).

Fidel Ramirez

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Ok, I will write a wrapper tomorrow. Do we care about renaming the tool? It does not fit the deepTools naming schema.

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I don't mind at all. Shall we call it can call it bamPEFragmentSize?

On Thu, Sep 4, 2014 at 4:34 PM, Björn Grüning [email protected]
wrote:

Ok, I will write a wrapper tomorrow. Do we care about renaming the tool?
It does not fit the deepTools naming schema.

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#45 (comment).

Fidel Ramirez

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Yes, something along these lines.

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