Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 51:e35b82f31ec7 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 08 Aug 2019 07:40:36 -0400 |
| parents | 2e3de43ff471 |
| children | 124b7fd92a3e |
| files | README.md igblast/igblast.sh |
| diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/README.md Wed Jul 10 03:38:24 2019 -0400 +++ b/README.md Thu Aug 08 07:40:36 2019 -0400 @@ -1,6 +1,7 @@ # ARGalaxy Immune Repertoire This is the GitHub repository for the ARGalaxy Immune repertoire pipeline. -The Galaxy tool version can be found [here](https://toolshed.g2.bx.psu.edu/repository/browse_repositories_i_own?sort=name&operation=view_or_manage_repository&id=2e457d63170a4b1c). +The Galaxy tool version can be found [here](https://toolshed.g2.bx.psu.edu/repository/browse_repositories_i_own?sort=name&operation=view_or_manage_repository&id=2e457d63170a4b1c). +The docker version can be found [here](https://github.com/ErasmusMC-Bioinformatics/ARGalaxy-docker). ## Overview
--- a/igblast/igblast.sh Wed Jul 10 03:38:24 2019 -0400 +++ b/igblast/igblast.sh Thu Aug 08 07:40:36 2019 -0400 @@ -23,6 +23,6 @@ echo "$input $species $locus $output" -java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1 +java -Xmx16G -jar $dir/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1