last fixes,all working now.Prepare for integration with SeqId-script

cyverseuk · Mar 14, 2017 · 484c2e4 · 484c2e4
1 parent 06dc187
commit 484c2e4
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diff --git a/agave/Phenotypes_Condor_submit.htc b/agave/Phenotypes_Condor_submit.htc
@@ -1,5 +1,5 @@
 universe = docker
-docker_image = teatree/retrieve_bip_phenotypes:v0.0.4
+docker_image = teatree/retrieve_bip_phenotypes:v0.0.6
 
 output = BIP-phenotypes.out
 error = BIP-phenotypes.err

diff --git a/retrieve_trial.sh b/retrieve_trial.sh
@@ -13,6 +13,7 @@ echo "Start running ruby client"
 ruby /usr/src/app/retrieve_phenotypes_and_ID.rb $trial_name $api_key
 
 echo "Extract sequence identifiers"
-cat Phenotypes_BIP_${trial_name}.csv| tr ',' '\t'|awk '{print $1 "," $2}' >> Seq_names.txt
+./ExtractSeqIds.sh
+
 
 echo "all done"