Added scripts for running inparanoid and copying the cvs repo from cshl to OSU

svn path=/; revision=5

diff --git a/server_admin_scripts/run_inparanoid.sh b/server_admin_scripts/run_inparanoid.sh
new file mode 100755 (executable)
index 0000000..5b0a014
--- /dev/null
+++ b/server_admin_scripts/run_inparanoid.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+
+lsarray=(`ls *.fa`)
+len=${#lsarray[@]}
+
+for (( i=0; i<$len; i++))
+do
+       for (( j=$i+1; j<$len; j++ ))
+       do
+               dirname=${lsarray[$i]}_______${lsarray[$j]}
+               echo $dirname
+               mkdir $dirname
+               cp ${lsarray[$i]} ${lsarray[$j]} $dirname
+               cd $dirname
+               cp ../../inparanoid.pl ./
+               cp ../../blast_parser.pl ./
+               cp ../../BLOSUM62 ./
+               cp ../../InparanoidXMLCreator.pl ./
+               cp ../../seqstat.jar ./
+               echo '#!/bin/bash
+#$ -cwd
+/usr/bin/perl inparanoid.pl '${lsarray[$i]} ${lsarray[$j]}'' > inparanoid_sub
+#              qsub inparanoid_sub
+               cd ..
+       done
+done

diff --git a/server_admin_scripts/run_inparanoid_fixed.sh b/server_admin_scripts/run_inparanoid_fixed.sh
new file mode 100755 (executable)
index 0000000..3d5b020
--- /dev/null
+++ b/server_admin_scripts/run_inparanoid_fixed.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+for dirname in /export/inparanoid_data/8_21_2009/*____*
+do
+cd $dirname
+#qsub inparanoid_sub
+command=`cat inparanoid_sub | grep inpara`
+$command
+
+done

diff --git a/server_admin_scripts/svnupdate.sh b/server_admin_scripts/svnupdate.sh
new file mode 100755 (executable)
index 0000000..a03dc71
--- /dev/null
+++ b/server_admin_scripts/svnupdate.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+machine=`uname -n`
+if [ $machine = palea.cgrb.oregonstate.edu ]; then
+       ssh brebiou.cshl.edu "cd /home/cvs; tar zcf ~/brebiou_cvsroot.tar.gz ./CVSROOT; tar zcf ~/Poc.tar.gz ./Poc"
+       echo "sudo password:"
+       sudo scp elserj@brebiou.cshl.edu:~/brebiou_cvsroot.tar.gz /data/svnrepos/cvs_files/brebiou/
+       sudo scp elserj@brebiou.cshl.edu:~/Poc.tar.gz /data/svnrepos/cvs_files/brebiou/
+       cd /data/svnrepos/cvs_files/brebiou
+       sudo tar zxf brebiou_cvsroot.tar.gz
+       sudo tar zxf Poc.tar.gz
+       sudo mv /data/svnrepos/Poc /data/svnrepos/Poc.old
+       sudo /home/bpp/elserj/cvs/cvs2svn-2.2.0/cvs2svn -s /data/svnrepos/Poc Poc --fallback-encoding=utf-8
+       sudo chown -R apache:apache /data/svnrepos
+       sudo chown root:root /data/svnrepos/passwords
+
+
+       ssh formaggio.cshl.edu "cd /usr/local/cvs_repository; tar zcf ~/formaggio_cvsroot.tar.gz ./CVSROOT; tar zcf ~/plantontology.tar.gz ./plantontology" 
+       echo "sudo password:"
+       sudo scp elserj@formaggio.cshl.edu:~/formaggio_cvsroot.tar.gz /data/svnrepos/cvs_files/formaggio/
+       sudo scp elserj@formaggio.cshl.edu:~/plantontology.tar.gz /data/svnrepos/cvs_files/formaggio/
+       cd /data/svnrepos/cvs_files/formaggio
+       sudo tar zxf formaggio_cvsroot.tar.gz
+       sudo tar zxf plantontology.tar.gz
+       sudo mv /data/svnrepos/plantontology /data/svnrepos/plantontology.old
+       sudo /home/bpp/elserj/cvs/cvs2svn-2.2.0/cvs2svn -s /data/svnrepos/plantontology plantontology --fallback-encoding=utf-8
+       sudo chown -R apache:apache /data/svnrepos
+       sudo chown root:root /data/svnrepos/passwords
+else
+       echo "This script must be ran from palea"
+fi