changeset 51:e35b82f31ec7 draft

Uploaded
author davidvanzessen
date Thu, 08 Aug 2019 07:40:36 -0400 (2019-08-08)
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