optionally break maf in pieces before Rnacode call #697

bernt-matthias · 2018-03-09T11:59:26Z

Uses breakMAF.pl (from RNAcode package) to break the alignment into pieces. Unfortunately the perl script seems to be missing in the conda package.

Of course we could also have a separate tool (but I don't see if splitting is interesting somewhere else).

…axytools into rnacode-break

bgruening

@bernt-matthias please also increase the tool version to 0.3.1. I guess we should add the perl script to the conda package.

bgruening · 2018-03-09T12:37:52Z

tools/rna_tools/rnacode/rnacode.xml

@@ -10,6 +10,15 @@
    <version_command>RNAcode --version</version_command>
    <command>


Can we use detect_errors here and remove the stdio?

should be fine

bgruening · 2018-03-09T12:38:09Z

tools/rna_tools/rnacode/rnacode.xml

+            breakMAF.pl
+            --maxlength $cond_breakmaf.maxlength
+            --desiredLength $cond_breakmaf.desiredLength
+            < $alignment > aln &&


alignment should be single quoted

- single quotes for alignment file - version increased - stdio -> detect_errors="exit_code"

bernt-matthias · 2018-03-09T13:03:31Z

could you update the conda package?

bgruening · 2018-03-09T13:06:03Z

Yes I can, but this take some time :(

and fixes

bernt-matthias · 2018-03-23T13:02:27Z

Since breakMAF.pl did not help with the RNAcode bug (ViennaRNA/RNAcode#8) I wrote a shell script that processes each part of split maf separately (which could also open some possibilities for parallel processing). I left this option optional. I added the breakMAF.pl since it seems not to be included in the latest release of RNAcode, but is only available from github.

bernt-matthias · 2018-03-23T13:04:32Z

I'm not so happy with creating a copy of the maf in the beginning of the script .. any thoughts on this?

Also replacing '.' by '-' (ViennaRNA/RNAcode#7) could be implemented easily .. but this could also be handled by a separate tool.

bgruening · 2018-03-23T20:51:03Z

tools/rna_tools/rnacode/rnacode.xml

-        RNAcode
-
+        #if $cond_breakmaf.select_breakmaf == 'breakmaf'
+            $__tool_directory__/breakMAF.pl


This one should be quoted.

@bgruening if I quote $cond_breakmaf.select_breakmaf then it does not work (i.e. the else path is used all the time). I guess you meant to quote something else?

@bernt-matthias You need to quote $__tool_directory__/breakMAF.pl, i.e. '$__tool_directory__/breakMAF.pl' , since $__tool_directory__ may contain spaces.

bgruening · 2018-03-23T20:51:16Z

tools/rna_tools/rnacode/rnacode.xml

+        #end if
+
+        #if $cond_breakmaf.select_breakmaf == 'breakmaf' and $cond_breakmaf.processseparately == 'yes'
+            $__tool_directory__/processMAF.sh


bgruening · 2018-03-23T20:54:10Z

Which copy? Does a symlink work?

bernt-matthias · 2018-03-25T19:52:35Z

I meant the 'copy' created by breakMAF.pl. I was thinking about using a named pipe. But I'm unsure how this needs to be used. I guess breakMAF would need to run in the background. I also don't know if RNAcode takes input from stdin...

bernt-matthias · 2018-03-27T16:54:12Z

@bgruening another question calling the perl and bash scripts directly caused an error because execute rights are needed for others (our galaxy runs jobs as real user). should I always use bash SCRIPT or perl SCRIPT for the calls?

bgruening · 2018-03-27T17:44:45Z

@bgruening another question calling the perl and bash scripts directly caused an error because execute rights are needed for others

This smells like chmod +x on the conda side?
Don't worry about the copying right now. The files are not that big isn't it.

bernt-matthias · 2018-03-28T06:45:36Z

@bgruening we will apply it on the hg38 alignments with 20 or 99 other mammals .. quite large :)

bgruening · 2018-03-28T06:49:02Z

Seriously? Crazy :)
But I don't have a better option at hand.

bgruening · 2018-04-12T14:41:13Z

You call. Merge?

bernt-matthias · 2018-04-13T09:04:21Z

Hoping that this is a good idea: galaxyproject/galaxy#5884 I switched to pipes. I'm fine to merge. If you think its not a good idea we can revert the last commit.

bgruening · 2018-04-13T12:30:02Z

Available from the toolshed and usegalaxy.eu.
Thanks!

bernt-matthias added 3 commits March 9, 2018 12:53

added optional call to breakMAF.pl before RNAcode

88749ff

added optional call to breakMAF.pl before RNAcode

a55a819

Merge branch 'rnacode-break' of https://github.com/bernt-matthias/gal…

0900a45

…axytools into rnacode-break

bgruening reviewed Mar 9, 2018

View reviewed changes

fixes

170ec5a

- single quotes for alignment file - version increased - stdio -> detect_errors="exit_code"

bernt-matthias added 2 commits March 22, 2018 15:23

preprocessing scripts and eps output working

503a14b

added processMAF for separate processing of parts

a103705

and fixes

bugfixes for gtf output

78beeaf

bgruening reviewed Mar 23, 2018

View reviewed changes

bernt-matthias added 2 commits March 26, 2018 08:20

added missing quotes

e495ea9

removed quotes again

644db01

applied correct quoting

7bf92b9

switched to pipes

16cc0a9

bgruening merged commit b6d3800 into bgruening:master Apr 13, 2018

bernt-matthias mentioned this pull request Jun 7, 2018

Catching warnings with regex #637

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optionally break maf in pieces before Rnacode call #697

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bgruening commented Apr 13, 2018

		@@ -10,6 +10,15 @@
		<version_command>RNAcode --version</version_command>
		<command>

optionally break maf in pieces before Rnacode call #697

optionally break maf in pieces before Rnacode call #697

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