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cancerit / cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
http://cancerit.github.io/cgpPindel/
GNU Affero General Public License v3.0
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using the docker container of cgpPINDEL #64

Closed tanasa closed 6 years ago

tanasa commented 6 years ago

Dear Keiran, and all,

if I may re-open an old message, thought that i may ask please which precise steps shall I follow in order to be able to use cgpPINDEL from a dockstore repository :

https://github.com/cancerit/dockstore-cgpwgs

I would very much appreciate your help. Thanks a lot,

-- bogdan

keiranmraine commented 6 years ago

If using via singularity or docker directly (not via CWL) replacing ds-cgpwgs.pl ... with pindel.pl -h will list the options you need to define.

You will need to expand the relevant reference archives and present them as a mounted file-system for this to be possible:

mkdir ref
tar --strip-components=1 -C ref -zxf ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/core_ref_GRCh37d5.tar.gz
tar --strip-components=1 -C ref -zxf ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/SNV_INDEL_ref_GRCh37d5-fragment.tar.gz