Changes between Version 58 and Version 59 of SopConvertLifeLinesGenoData

Timestamp:

2013-02-08T08:22:15+01:00 (12 years ago)

Author:

Morris Swertz

Comment:

--

SopConvertLifeLinesGenoData

@@ -174 +174 @@
 2. Find compiled jars at http://www.molgenis.org/svn/standalone_tools/jars/
 2. Read manuals for use: http://www.molgenis.org/svn/standalone_tools/manuals/
+
+= Additional scripts ==
+
+Define the source folders (where data has been converted) and final destination (folder where data is served). Sometimes the name are different.
+
+For example
+
+{{{
+sources=("lifelines_OV0xy" "lifelines_OV0xy")
+targets=("lifelines_OV0ab" "lifelines_OV0cd")
+}}}
+
+Script to check if all folders are there
+
+{{{
+total=${#sources[*]}
+for (( i=0; i<=$(( $total -1 )); i++ )) do
+if [ -d /target/gpfs2/lifelines-genome/home/${targets[i]}/ ] && [ -d /target/gpfs2/lifelines_rp/releases/LL3/${sources[i]}/ ]; then
+echo ${targets[i]}
+else
+echo "error: "${sources[i]}
+fi
+}}}
+
+Batch copy and setup of the data
+
+{{{
+
+total=${#sources[*]}
+for (( i=0; i<=$(( $total -1 )); i++ )) do
+if [ -d /target/gpfs2/lifelines-genome/home/${targets[i]}/ ] && [ -d /target/gpfs2/lifelines_rp/releases/LL3/${sources[i]}/ ]; then
+echo ${targets[i]}
+
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*.bim
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*.ped
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*.map
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*.bed
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*.dose
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*.log
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*.fam
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/*_imputation*
+
+rsync -av --progress /target/gpfs2/lifelines_rp/releases/LL3/${sources[i]}/ \
+/target/gpfs2/lifelines-genome/home/${targets[i]}/
+
+rm /target/gpfs2/lifelines-genome/home/${targets[i]}/temp*
+chown -R $user /target/gpfs2/lifelines-genome/home/${targets[i]}/*
+chmod -R a-rw /target/gpfs2/lifelines-genome/home/${targets[i]}/*
+chmod -R u+r /target/gpfs2/lifelines-genome/home/${targets[i]}/*
+
+else
+echo "error: "${sources[i]}
+fi
+done
+}}}