Improved file system layout when running on Jetstream

feltus · 0d942b4974992affc2d83cdf42334a493321028e · mats@rynge.net committed Dec 16, 2016 · Dec 16, 2016 · 0d942b4
1 parent b428b9d
commit 0d942b4974992affc2d83cdf42334a493321028e
Unified Split

Showing with 6 additions and 4 deletions.

+2 −0 .gitignore

+2 −2 sites.xml.template

+1 −1 submit

+1 −1 tools/sra-download
diff --git a/.gitignore b/.gitignore
@@ -11,4 +11,6 @@ reference/*.txt
 reference/*.gtf
 tools/AutoADAG.pyc
 osg-gem.conf
+staging
+runs
 
diff --git a/sites.xml.template b/sites.xml.template
@@ -36,8 +36,8 @@
     </site>
     
     <site  handle="jetstream-staging" arch="x86_64" os="LINUX">
-        <directory type="shared-scratch" path="/tmp/staging-${USER}">
-            <file-server operation="all" url="scp://${USER}@${HOSTNAME}/tmp/staging-${USER}"/>
+        <directory type="shared-scratch" path="${PWD}/staging">
+            <file-server operation="all" url="scp://${USER}@${HOSTNAME}${PWD}/staging"/>
         </directory>
     </site>
 
diff --git a/submit b/submit
@@ -55,7 +55,7 @@ else
     
     export RUN_ID=osg-gem-`date +'%s'`
     
-    export RUN_DIR=$HOME/workflows/$RUN_ID
+    export RUN_DIR=$PWD/runs/$RUN_ID
     mkdir -p $RUN_DIR/scratch/$RUN_ID/level-2
     mkdir -p $RUN_DIR/data
     
diff --git a/tools/sra-download b/tools/sra-download
@@ -8,7 +8,7 @@
 set -e
 
 module load java/8u25
-module load sra/2.5.4
+module load sra/2.8.0
 
 SRA_ID=$1
 FORWARD=$2