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Need wrapper scripts for BWA PE and SE module #2

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I'm beginning to test the BWA PE & SE Aligner modules on fgene1. First I'm 
converting them to fgene1-specific paths. 

To complete this step, Ivo, could I have a copy of these wrapper scripts from 
the CRANIUM-based pipeline?

/ifshome/shobel/scripts/BWA_aln.sh
/ifshome/shobel/scripts/bwa_sampe.sh

Also, as luck would have it, the very next version of BWA released after we 
wrote up the pipeline documents includes a new '-f' option to define an output 
file (eliminating the need for shell redirectors ">" in a wrapper script). 
There is also another essential new parameter, -I (an upper case 'i'), that 
eliminates the need for the MAQ sol2sanger step.

So I think it would be worthwhile to update our BWA module to include these 
nice features in the new version. I'll update the pipeline documentation first, 
though and follow up on that soon.

Original issue reported on code.google.com by apcexcha...@gmail.com on 20 Jul 2011 at 2:22

GoogleCodeExporter commented 9 years ago 
Hi Andrew and Federica - apologies for missing these scripts. You can find them 
here:

/raid/users/idinov/Pipeline_fgene_missingscripts.zip

 - Ivo

Original comment by iwaterp...@gmail.com on 20 Jul 2011 at 10:16

GoogleCodeExporter commented 9 years ago 
The missing scripts are attached (but may need to be slightly modified for the 
fgene Pipeline server environment).

Original comment by iwaterp...@gmail.com on 20 Jul 2011 at 10:28

Attachments:

GoogleCodeExporter commented 9 years ago 
There is a slight permissions obstacle preventing me from copying the .zip file:

cp: cannot stat `/raid/users/idinov/Pipeline_fgene_missingscripts.zip': 
Permission denied

I think it is the permission setting on /raid/users/idinov that is blocking me 
from accessing the pipeline .zip file. Can you add group read and execute 
permissions to your home directory, or copy the file to another location on 
/projects1 perhaps? 

Thanks!

Original comment by apcexcha...@gmail.com on 20 Jul 2011 at 11:14

GoogleCodeExporter commented 9 years ago 
Oops, sorry, not sure why this is protected, but here is an open copy:
/tmp/Pipeline_fgene_missingscripts.zip

Original comment by iwaterp...@gmail.com on 20 Jul 2011 at 11:46