From 066dee09478c87c83951c15cced72e604fb9db3d Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 22 Nov 2011 14:06:34 +0100 Subject: Added ambit_descriptors.yaml --- ambit_descriptors.yaml | 124 +++++++++++++++++++++++++++++++++++++++++++++++++ opentox-ruby.sh | 1 + 2 files changed, 125 insertions(+) create mode 100644 ambit_descriptors.yaml diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml new file mode 100644 index 0000000..19e66f9 --- /dev/null +++ b/ambit_descriptors.yaml @@ -0,0 +1,124 @@ +--- +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: + :category: "geometrical" + :name: "Length Over Breadth" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: + :category: "topological" + :name: "Kier & Hall SMARTS" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: + :category: "topological" + :name: "Fragment Complexity" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: + :category: "electronic" + :name: "Atomic Polarizabilities" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: + :category: "constitutional" + :name: "Largest Chain" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor: + :category: "topological" + :name: "Chi Path Indices" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: + :category: "topological" + :name: "Petitjean Number" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: + :category: "constitutional" + :name: "Longest Aliphatic Chain" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: + :category: "topological" + :name: "Kier and Hall kappa molecular shape indices" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: + :category: "constitutional" + :name: "Aromatic Bonds Count" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: + :category: "electronic" + :name: "Charged Partial Surface Areas" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: + :category: "topological" + :name: "Vertex adjacency information magnitude" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass: + :category: "topological" + :name: "Moreau-Broto Autocorrelation (mass) descriptors" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: + :category: "constitutional" + :name: "Lipinski's Rule of Five" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: + :category: "geometrical" + :name: "Gravitational Index" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: + :category: "topological" + :name: "Wiener Numbers" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor: + :category: "topological" + :name: "Chi Path-Cluster Indices" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: + :category: "constitutional" + :name: "Atoms Count" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: + :category: "geometrical" + :name: "Moments of Inertia" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: + :category: "topological" + :name: "Carbon Types" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability: + :category: "topological" + :name: "Moreau-Broto Autocorrelation (polarizability) descriptors" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: + :category: "topological" + :name: "Eccentric Connectivity Index" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: + :category: "hybrid" + :name: "BCUT" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: + :category: "constitutional" + :name: "Aromatic Atoms Count" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: + :category: "hybrid" + :name: "WHIM" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor: + :category: "constitutional" + :name: "ALogP" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: + :category: "constitutional" + :name: "XLogP" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: + :category: "topological" + :name: "Petitjean Number" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: + :category: "topological" + :name: "Molecular Distance Edge" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor: + :category: "topological" + :name: "Chi Chain Indices" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: + :category: "constitutional" + :name: "Bonds Count" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: + :category: "constitutional" + :name: "Mannhold LogP" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: + :category: "electronic" + :name: "Bond Polarizabilities" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge: + :category: "topological" + :name: "Moreau-Broto Autocorrelation (charge) descriptors" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: + :category: "topological" + :name: "Zagreb Index" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor: + :category: "topological" + :name: "Chi Cluster Indices" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: + :category: "constitutional" + :name: "Rotatable Bonds Count" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: + :category: "topological" + :name: "Topological Polar Surface Area" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: + :category: "electronic" + :name: "Hydrogen Bond Donors" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: + :category: "electronic" + :name: "Hydrogen Bond Acceptors" +http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: + :category: "constitutional" + :name: "Largest Pi Chain" diff --git a/opentox-ruby.sh b/opentox-ruby.sh index ec7f5c2..d53d5ba 100755 --- a/opentox-ruby.sh +++ b/opentox-ruby.sh @@ -73,6 +73,7 @@ $GIT checkout aa-$OT_INSTALL.yaml >>$LOG 2>&1 cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1" cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2" +cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit" if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then mkdir -p $WWW_DEST/opentox >>$LOG 2>&1 -- cgit v1.2.3 From 7acb3bc7db272581b9055c8e073aa7b07206f6fe Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Wed, 23 Nov 2011 09:49:21 +0100 Subject: Minor improvements --- opentox-webservices.sh | 8 ++++---- update | 16 ---------------- 2 files changed, 4 insertions(+), 20 deletions(-) delete mode 100755 update diff --git a/opentox-webservices.sh b/opentox-webservices.sh index cc53d04..88f864c 100755 --- a/opentox-webservices.sh +++ b/opentox-webservices.sh @@ -65,21 +65,21 @@ cmd="$GIT submodule update" && run_cmd "$cmd" "Fminer Update" cd "libfminer/libbbrc">>$LOG 2>&1 $GIT checkout $OT_BRANCH>>$LOG 2>&1 $GIT pull >>$LOG 2>&1 -cd - +cd - >>$LOG 2>&1 cd "libfminer/liblast">>$LOG 2>&1 $GIT checkout $OT_BRANCH>>$LOG 2>&1 $GIT pull >>$LOG 2>&1 -cd - +cd - >>$LOG 2>&1 for mylib in bbrc last; do cmd="sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ -I$OB_DEST/include/openbabel-2.0,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile; sed -i 's,^LDFLAGS_OB.*,LDFLAGS_OB\ =\ -L$OB_DEST/lib,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (OB)" cmd="sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ -I$RUBY_DEST/lib/ruby/1.8/`uname -m`-linux,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (RB)" done cd "libfminer/libbbrc">>$LOG 2>&1 cmd="make ruby" && run_cmd "$cmd" "Make BBRC" -cd - +cd - >>$LOG 2>&1 cd "libfminer/liblast">>$LOG 2>&1 cmd="make ruby" && run_cmd "$cmd" "Make LAST" -cd - +cd - >>$LOG 2>&1 cd "last-utils">>$LOG 2>&1 $GIT checkout $OT_BRANCH>>$LOG 2>&1 $GIT pull >>$LOG 2>&1 diff --git a/update b/update deleted file mode 100755 index 77183ed..0000000 --- a/update +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/sh -. /etc/profile -gem update opentox-ruby -dir=`pwd` -cd /var/www/opentox -for s in *; do - echo $s - cd $s - git pull - cd - -done -cd /var/www/algorithm -rake fminer:update -kill `cat /opt/nginx/logs/nginx.pid` -/opt/nginx/sbin/nginx -cd $dir -- cgit v1.2.3 From 7d7a277cd3c2a56a044aa5364c3a651e03a60652 Mon Sep 17 00:00:00 2001 From: ot1 Date: Wed, 30 Nov 2011 08:52:54 +0100 Subject: Supporting MLR install --- kernlab.sh | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/kernlab.sh b/kernlab.sh index 511874b..8139747 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -45,13 +45,17 @@ else fi -if ! $R_DONE; then +if $R_DONE; then cd $HOME/tmp + export R_LIBS="$KL_DEST" # To install non-global + URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz" - cmd="$WGET $URI" && run_cmd "$cmd" "Download" + cmd="$WGET $URI" && run_cmd "$cmd" "Download KL" + cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install KL" - export R_LIBS="$KL_DEST" # To install non-global - cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install" + URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz" + cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" + cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install PLS" fi -- cgit v1.2.3 From 582753e3f256b7b9329dd6750731ed7a27ae5b87 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 5 Dec 2011 13:55:49 +0100 Subject: Fixed backup. --- install | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/install b/install index 705ff44..a486660 100755 --- a/install +++ b/install @@ -14,21 +14,22 @@ read help_var echo mkdir -p $HOME/tmp/ >/dev/null 2>&1 +DATE=`date +_%Y%m%d_%H_%M` if [ -f "$HOME/.opentox-ui.sh" ] then - mv -b -v $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh~ + mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE else echo "$HOME/.opentox-ui.sh does not found (nothing to backup)." fi if [ -d "$HOME/.opentox" ] then - mv -b -v -T $HOME/.opentox $HOME/.opentox~ + mv -v --backup=numbered -T $HOME/.opentox $HOME/.opentox$DATE else echo "$HOME/.opentox does not found (nothing to backup)." fi if [ -d "$HOME/opentox-ruby" ] then - mv -b -v -T $HOME/opentox-ruby $HOME/opentox-ruby~ + mv -v --backup=numbered -T $HOME/opentox-ruby $HOME/opentox-ruby$DATE else echo "$HOME/opentox-ruby does not found (nothing to backup)." fi -- cgit v1.2.3 From 4ad029cf4123a436822bd829a42e87ff9b634ef0 Mon Sep 17 00:00:00 2001 From: ot1 Date: Mon, 5 Dec 2011 14:59:31 +0100 Subject: Added RB --- kernlab.sh | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/kernlab.sh b/kernlab.sh index 8139747..52006dc 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -55,7 +55,11 @@ if $R_DONE; then URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" - cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install PLS" + cmd="$R CMD INSTALL pls_2.3.0.tar.gz" && run_cmd "$cmd" "Install PLS" + + URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz" + cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" + cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB" fi -- cgit v1.2.3 From 13218d2158ace60f02d0d2d4b0bbaf4f980c61c3 Mon Sep 17 00:00:00 2001 From: ot1 Date: Mon, 5 Dec 2011 15:00:42 +0100 Subject: Fixed installation of pls --- kernlab.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kernlab.sh b/kernlab.sh index 8139747..4faf08c 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -55,7 +55,7 @@ if $R_DONE; then URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" - cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install PLS" + cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS" fi -- cgit v1.2.3 From 23cd09e039577124fa27b5b0f72509dd058bd308 Mon Sep 17 00:00:00 2001 From: davor Date: Mon, 5 Dec 2011 15:25:10 +0100 Subject: Fixed if statement. --- kernlab.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kernlab.sh b/kernlab.sh index 4faf08c..582950f 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -45,7 +45,7 @@ else fi -if $R_DONE; then +if ! $R_DONE; then cd $HOME/tmp export R_LIBS="$KL_DEST" # To install non-global -- cgit v1.2.3 From 0924b25654d554a5c6a3fa99e6902227dfe0f6d3 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Wed, 7 Dec 2011 10:30:50 +0100 Subject: Added LEAPS package --- kernlab.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/kernlab.sh b/kernlab.sh index f73d376..3ee6aff 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -60,6 +60,10 @@ if ! $R_DONE; then URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB" + + URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz" + cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS" + cmd="$R CMD INSTALL leaps_2.9.tar.gz" && run_cmd "$cmd" "Install LEAPS" fi -- cgit v1.2.3 From 4de5abc3c49d8cdb01866f5a038e9a1597fb5ae8 Mon Sep 17 00:00:00 2001 From: davor Date: Fri, 9 Dec 2011 16:39:14 +0100 Subject: Fixed typo --- kernlab.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kernlab.sh b/kernlab.sh index 3ee6aff..11e5637 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -55,7 +55,7 @@ if ! $R_DONE; then URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" - cmd="$R CMD INSTALL pls_2.3.0.tar.gz" && run_cmd "$cmd" "Install PLS" + cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS" URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" -- cgit v1.2.3 From 89658d67203e00dedd2a795fceb61d954d07b2d5 Mon Sep 17 00:00:00 2001 From: davor Date: Sun, 11 Dec 2011 22:17:06 +0100 Subject: Updated download path to new version (robustbase_0.8-0) --- kernlab.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/kernlab.sh b/kernlab.sh index 11e5637..c4fc206 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -57,9 +57,9 @@ if ! $R_DONE; then cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS" - URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz" + URI="http://cran.r-project.org/src/contrib/robustbase_0.8-0.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" - cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB" + cmd="$R CMD INSTALL robustbase_0.8-0.tar.gz" && run_cmd "$cmd" "Install RB" URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS" -- cgit v1.2.3 From d56d27d7e7804521c8b8dce7c273fbb4e5ddd86c Mon Sep 17 00:00:00 2001 From: davor Date: Mon, 12 Dec 2011 10:58:18 +0100 Subject: Changed download path to archive version --- kernlab.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/kernlab.sh b/kernlab.sh index c4fc206..a833bd9 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -57,9 +57,9 @@ if ! $R_DONE; then cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS" - URI="http://cran.r-project.org/src/contrib/robustbase_0.8-0.tar.gz" + URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" - cmd="$R CMD INSTALL robustbase_0.8-0.tar.gz" && run_cmd "$cmd" "Install RB" + cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB" URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz" cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS" -- cgit v1.2.3 From 600466723755e0440fff0f908bfddc2ef3f05fa5 Mon Sep 17 00:00:00 2001 From: davor Date: Mon, 12 Dec 2011 11:43:08 +0100 Subject: Removed static download url for r packages. They have to be downloaded manually (only temporarily). --- kernlab.sh | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/kernlab.sh b/kernlab.sh index a833bd9..c4bafbd 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -53,16 +53,20 @@ if ! $R_DONE; then cmd="$WGET $URI" && run_cmd "$cmd" "Download KL" cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install KL" - URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz" - cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" + + echo "Warning! If you already downloaded pls_2.3-0.tar.gz , robustbase_0.7-8.tar.gz and leaps_2.9.tar.gz from http://cran.r-project.org/src/contrib/ into $HOME/tmp/ press return, else to stop installation." + read help_var2 + echo + #URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz" + #cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS" - URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz" - cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" + #URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz" + #cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB" - URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz" - cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS" + #URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz" + #cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS" cmd="$R CMD INSTALL leaps_2.9.tar.gz" && run_cmd "$cmd" "Install LEAPS" fi -- cgit v1.2.3 From 4a6edd6921869f5ab53acd882f3bff276c31463a Mon Sep 17 00:00:00 2001 From: davor Date: Thu, 29 Dec 2011 16:19:03 +0100 Subject: cpsa in own category --- ambit_descriptors.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml index 19e66f9..1e2c347 100644 --- a/ambit_descriptors.yaml +++ b/ambit_descriptors.yaml @@ -30,7 +30,7 @@ http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descr :category: "constitutional" :name: "Aromatic Bonds Count" http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: - :category: "electronic" + :category: "cpsa" :name: "Charged Partial Surface Areas" http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: :category: "topological" -- cgit v1.2.3 From b6fb537437568bdf274451554663d8273151ffe8 Mon Sep 17 00:00:00 2001 From: davor Date: Mon, 16 Jan 2012 13:12:26 +0100 Subject: fixed search param -S for already installed packs --- base-install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base-install.sh b/base-install.sh index 90abb6e..a1ee2bf 100644 --- a/base-install.sh +++ b/base-install.sh @@ -34,7 +34,7 @@ echo "Base Packages:" pack_arr="" for p in $packs; do - if $DPKG -s "$p" >/dev/null 2>&1; then + if $DPKG -S "$p" >/dev/null 2>&1; then printf "%50s%30s\n" "'$p'" "Y" else printf "%50s%30s\n" "'$p'" "N" -- cgit v1.2.3 From 2e53016f91abb5af7e9cd24f336fce5f121c92ae Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 31 Jan 2012 09:04:16 +0100 Subject: Adjusted R installation --- config.sh | 4 ++-- kernlab.sh | 46 ++++++++++++++-------------------------------- 2 files changed, 16 insertions(+), 34 deletions(-) diff --git a/config.sh b/config.sh index 60dff2a..b553594 100755 --- a/config.sh +++ b/config.sh @@ -34,7 +34,7 @@ RUBY_CONF="$OT_PREFIX/.sh_ruby_ot" REDIS_CONF="$OT_PREFIX/.sh_redis_ot" NGINX_CONF="$OT_PREFIX/.sh_nginx_ot" OB_CONF="$OT_PREFIX/.sh_OB_ot" -KL_CONF="$OT_PREFIX/.sh_R_ot" +R_CONF="$OT_PREFIX/.sh_R_ot" RUBY_VER="ruby-enterprise-$RUBY_NUM_VER" OB_VER="openbabel-$OB_NUM_VER" @@ -44,7 +44,7 @@ REDIS_VER="$REDIS_NUM_VER" RUBY_DEST="$OT_PREFIX/$RUBY_VER" OB_DEST="$OT_PREFIX/$OB_VER" OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install" -KL_DEST="$OT_PREFIX/r-packages" +R_DEST="$OT_PREFIX/r-packages" NGINX_DEST="$OT_PREFIX/nginx" REDIS_DEST="$OT_PREFIX/redis-$REDIS_VER" diff --git a/kernlab.sh b/kernlab.sh index c4bafbd..2df0b8e 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -32,53 +32,35 @@ echo echo "Kernlab ('$LOG')." R_DONE=false -mkdir "$KL_DEST" >/dev/null 2>&1 -if [ ! -d "$KL_DEST" ]; then - echo "Install directory '$KL_DEST' is not available! Aborting..." +mkdir "$R_DEST" >/dev/null 2>&1 +if [ ! -d "$R_DEST" ]; then + echo "Install directory '$R_DEST' is not available! Aborting..." exit 1 else - if ! rmdir "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail + if ! rmdir "$R_DEST" >/dev/null 2>&1; then # if not empty this will fail R_DONE=true else - mkdir "$KL_DEST" >/dev/null 2>&1 + mkdir "$R_DEST" >/dev/null 2>&1 fi fi if ! $R_DONE; then cd $HOME/tmp - export R_LIBS="$KL_DEST" # To install non-global - - URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz" - cmd="$WGET $URI" && run_cmd "$cmd" "Download KL" - cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install KL" - - - echo "Warning! If you already downloaded pls_2.3-0.tar.gz , robustbase_0.7-8.tar.gz and leaps_2.9.tar.gz from http://cran.r-project.org/src/contrib/ into $HOME/tmp/ press return, else to stop installation." - read help_var2 - echo - #URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz" - #cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS" - cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS" - - #URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz" - #cmd="$WGET $URI" && run_cmd "$cmd" "Download RB" - cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB" - - #URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz" - #cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS" - cmd="$R CMD INSTALL leaps_2.9.tar.gz" && run_cmd "$cmd" "Install LEAPS" + export R_LIBS="$R_DEST" # To install non-global + options(repos="http://mirrors.softliste.de/cran") # set mirror to avoid questioning the user + install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape")) fi -if [ ! -f $KL_CONF ]; then +if [ ! -f $R_CONF ]; then - echo "if echo \"\$R_LIBS\" | grep -v \"$KL_DEST\">/dev/null 2>&1; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF" - echo "if ! [ -d \"$KL_DEST\" ]; then echo \"\$0: '$KL_DEST' is not a directory!\"; fi" >> "$KL_CONF" - echo "R package destination has been stored in '$KL_CONF'." + echo "if echo \"\$R_LIBS\" | grep -v \"$R_DEST\">/dev/null 2>&1; then export R_LIBS=\"$R_DEST\"; fi" >> "$R_CONF" + echo "if ! [ -d \"$R_DEST\" ]; then echo \"\$0: '$R_DEST' is not a directory!\"; fi" >> "$R_CONF" + echo "R package destination has been stored in '$R_CONF'." - if ! grep "$KL_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then - echo ". \"$KL_CONF\"" >> $OT_UI_CONF + if ! grep "$R_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then + echo ". \"$R_CONF\"" >> $OT_UI_CONF fi fi -- cgit v1.2.3 From 9282f0715873f96cf43c23261a808dc00fb78914 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 31 Jan 2012 10:07:01 +0100 Subject: Fixed R lib install --- config.sh | 2 -- install | 6 +++--- kernlab.sh | 5 ++--- packs.R | 6 ++++++ 4 files changed, 11 insertions(+), 8 deletions(-) create mode 100644 packs.R diff --git a/config.sh b/config.sh index b553594..afe2012 100755 --- a/config.sh +++ b/config.sh @@ -16,7 +16,6 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-sun" # 3) What versions to install. RUBY_NUM_VER="1.8.7-2011.03" OB_NUM_VER="2.2.3" -KL_NUM_VER="0.9-11" REDIS_NUM_VER="2.2.2" # 4) Server settings. @@ -38,7 +37,6 @@ R_CONF="$OT_PREFIX/.sh_R_ot" RUBY_VER="ruby-enterprise-$RUBY_NUM_VER" OB_VER="openbabel-$OB_NUM_VER" -KL_VER="$KL_NUM_VER" REDIS_VER="$REDIS_NUM_VER" RUBY_DEST="$OT_PREFIX/$RUBY_VER" diff --git a/install b/install index a486660..b0422b5 100755 --- a/install +++ b/install @@ -19,19 +19,19 @@ if [ -f "$HOME/.opentox-ui.sh" ] then mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE else - echo "$HOME/.opentox-ui.sh does not found (nothing to backup)." + echo "$HOME/.opentox-ui.sh not found (nothing to backup)." fi if [ -d "$HOME/.opentox" ] then mv -v --backup=numbered -T $HOME/.opentox $HOME/.opentox$DATE else - echo "$HOME/.opentox does not found (nothing to backup)." + echo "$HOME/.opentox not found (nothing to backup)." fi if [ -d "$HOME/opentox-ruby" ] then mv -v --backup=numbered -T $HOME/opentox-ruby $HOME/opentox-ruby$DATE else - echo "$HOME/opentox-ruby does not found (nothing to backup)." + echo "$HOME/opentox-ruby not found (nothing to backup)." fi LOG="$HOME/tmp/`basename $0`-log.txt" . "./utils.sh" diff --git a/kernlab.sh b/kernlab.sh index 2df0b8e..aad125d 100755 --- a/kernlab.sh +++ b/kernlab.sh @@ -46,10 +46,9 @@ fi if ! $R_DONE; then - cd $HOME/tmp export R_LIBS="$R_DEST" # To install non-global - options(repos="http://mirrors.softliste.de/cran") # set mirror to avoid questioning the user - install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape")) + cmd="$R CMD BATCH packs.R" && run_cmd "$cmd" "R packages" + eval "$cmd" fi diff --git a/packs.R b/packs.R new file mode 100644 index 0000000..b130360 --- /dev/null +++ b/packs.R @@ -0,0 +1,6 @@ +# CRAN package installer for opentox-ruby +# AM, 2012 + +# set mirror to avoid questioning the user +options(repos="http://mirrors.softliste.de/cran") +install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape")) -- cgit v1.2.3 From ca56463e893e0d058dc5571e673d2fbfe14508b2 Mon Sep 17 00:00:00 2001 From: davor Date: Thu, 9 Feb 2012 09:29:22 +0100 Subject: Added R packages: "randomForest","RANN" --- packs.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packs.R b/packs.R index b130360..b6b1930 100644 --- a/packs.R +++ b/packs.R @@ -3,4 +3,4 @@ # set mirror to avoid questioning the user options(repos="http://mirrors.softliste.de/cran") -install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape")) +install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape", "randomForest", "RANN")) -- cgit v1.2.3