rbbt-image 0.1.35 → 0.1.36

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c7c7d21c1945100f43485cec703a2af72e181e7d91589395e08e1cb07d430a93
-  data.tar.gz: 06d21330a2d93254ac61ca1f7cc8432790b2ab914bd69c7f0c40044288db5adf
+  metadata.gz: b6ed0fbc0b9b6ea6d4f6b7f1cd9931bebd8e5438ec37b5c73ecdaf545ffde7b2
+  data.tar.gz: 68e3073a6bd603fa0404fb3403ecf87c22c0731546b24afc4e2ea059b73a2acf
 SHA512:
-  metadata.gz: 7f6b918673bb5c735679713a1a2d689925580d642859782b828063776a6817266c1f372be5641f8a93da7058f83da5a1e455164a4ad104aa32842ce0d456a2f9
-  data.tar.gz: 6015203a7fb0abf5fb4145998c1acd87c2b7cdb957d94f27bf1bbdcebacd02ee4c5c1cf38dd3012653e6e878a98ba126954fdabdfae4d54f37ec63c4e04d91ef
+  metadata.gz: 288e7e36fed3c08d32416a88af59caffe684d5fdefdf22b5a9b5e1ea051f825c3b1e138932d787d797ff8aa142ff2d5b8a5d1481a28f6f4ca5388df956f231e8
+  data.tar.gz: 5910cee842328c52a9057b85184aaba2149d6d8427efd4e164448af75651ca2783a881e612b6517baba7dce920a3389236a04d1bc45b17bac9ff0770a0d6fcda

data/bin/build_rbbt_provision_sh.rb

@@ -119,9 +119,6 @@ else
 end 
 }
 
-echo "[ -f ~/.rbbt/etc/environment ] && . ~/.rbbt/etc/environment" >> "/etc/rbbt_environment"
-echo "source /etc/rbbt_environment" >> /etc/profile
-
 #{
 if not SKIP_BASE_SYSTEM and R_CUSTOM
   "echo 1.1 Setting custom R"
@@ -182,6 +179,9 @@ else
   "echo SKIPPED\necho"
 end 
 }
+
+echo "[ -f ~/.rbbt/etc/environment ] && . ~/.rbbt/etc/environment" >> "/etc/rbbt_environment"
+echo "source /etc/rbbt_environment" >> /etc/profile
 EOF
 
 provision_script +=<<-EOF

data/share/provision_scripts/R_setup.sh

@@ -15,9 +15,8 @@ cd R-*/
 make && make install
 
 echo "# For RSRuby gem " >> /etc/rbbt_environment
-echo "export R_HOME='/usr/local/lib/R'" >> /etc/rbbt_environment
-echo "export PATH=\"$R_HOME/bin:$PATH\"" >> /etc/rbbt_environment
-echo "export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:\$R_HOME/lib\"" >> /etc/rbbt_environment
-echo "export LD_RUN_PATH=\"\$LD_RUN_PATH:\$R_HOME/lib\"" >> /etc/rbbt_environment
+echo 'export R_HOME="/usr/local/lib/R"' >> /etc/rbbt_environment
+echo '_add_path "$R_HOME/bin/" # Rserver' >> /etc/rbbt_environment
+echo '_add_lib_path "$R_HOME/lib/" # Rserver' >> /etc/rbbt_environment
 
 . /etc/rbbt_environment

data/share/provision_scripts/python_setup.sh

@@ -1,15 +1,16 @@
 wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" -O /tmp/miniconda.sh
-bash /tmp/miniconda.sh -b -p /opt/miniconda3
+echo "# Python conda " >> /etc/rbbt_environment
 
-[ -d /opt/bin/conda ] || mkdir -p /opt/bin/conda
-ln -s /opt/miniconda3/bin/conda /opt/bin/conda
+bash /tmp/miniconda.sh -b -p /usr/local/miniconda3
+ln -s /usr/local/miniconda3/bin/conda /usr/local/bin/conda
+echo '_add_path "/usr/local/miniconda3/bin/"' >> /etc/rbbt_environment
 
-conda create --yes -n python3 python=3.6.1 pip
-rm -Rf /opt/miniconda3/pkgs
 conda create --yes -n python2 python=2.7 pip
-rm -Rf /opt/miniconda3/pkgs
 
-echo "# Python conda " >> /etc/rbbt_environment
-echo 'export PATH="/opt/bin/:/opt/miniconda3/envs/python3/bin/:$PATH"' >> /etc/rbbt_environment
+conda create --yes -n python3 python=3 pip
+
+echo '_add_path "/usr/local/miniconda3/envs/python2/bin/"' >> /etc/rbbt_environment
+echo '_add_path "/usr/local/miniconda3/envs/python3/bin/"' >> /etc/rbbt_environment
 
+rm -Rf /usr/local/miniconda3/pkgs
 source /etc/rbbt_environment

data/share/provision_scripts/ruby_setup.sh

@@ -13,7 +13,6 @@ make && make install
 
 unset _small_version
 
-echo 'export PATH="/usr/local/bin:/opt/bin:$PATH" #Ruby2' >> /etc/rbbt_environment
 . /etc/rbbt_environment
 
 #\curl -sSL https://get.rvm.io | bash -s stable

data/share/provision_scripts/ubuntu_setup.sh

@@ -3,6 +3,68 @@
 # INSTALL
 # =======
 
+cat << 'EOF' > /etc/rbbt_environment 
+_var_content(){
+    var=$1
+    eval echo "$"$(echo $var)
+}
+
+_append_with_colon(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" &> /dev/null; then
+        eval $(echo $var)="\"$current:$value\""
+    fi
+}
+
+_append_with_space(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\| \)$value\( \|$\)" &> /dev/null; then
+        eval $(echo $var)="\"$current:$value\""
+    fi
+}
+
+_prepend_with_colon(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" &> /dev/null; then
+        eval $(echo $var)="\"$value:$current\""
+    fi
+}
+
+_prepend_with_space(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\| \)$value\( \|$\)" &> /dev/null; then
+        eval $(echo $var)="\"$value $current\""
+    fi
+}
+
+_add_path(){
+  _prepend_with_colon PATH "$1"
+}
+
+_add_libpath(){
+  _prepend_with_colon LD_LIBRARY_PATH "$1"
+  _prepend_with_colon LD_RUN_PATH "$1"
+}
+EOF
+
+. /etc/rbbt_environment
+
 # Basic system requirements
 # -------------------------
 apt-get -y update
@@ -22,7 +84,7 @@ apt-get -y install \
   tcsh gawk \
   libtbb-dev
 
-add-apt-repository ppa:george-edison55/cmake-3.x
+#add-apt-repository ppa:george-edison55/cmake-3.x
 apt-get -y update
 apt-get -y update
 apt-get -y install cmake
@@ -36,12 +98,15 @@ rm /usr/lib/R/bin/Rserve
 ln -s /usr/lib/R/site-library/Rserve/libs/Rserve /usr/lib/R/bin/Rserve
 
 echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/rbbt_environment
-echo 'export PATH="$R_HOME/bin/:$PATH" # Rserver' >> /etc/rbbt_environment
+echo '_add_path "$R_HOME/bin/" # Rserver' >> /etc/rbbt_environment
+
+[ -d /opt/bin ] || mkdir -p /opt/bin
+echo '_add_path "/opt/bin/"' >> /etc/rbbt_environment
+
+[ -d /usr/local/bin ] || mkdir -p /usr/local/bin
+echo '_add_path "/usr/local/bin/"' >> /etc/rbbt_environment
 
 . /etc/rbbt_environment
 
 apt-get clean
 rm -rf /var/lib/apt/lists/* 
-
-
-

data/share/provision_scripts/variables.sh

@@ -1,6 +1,6 @@
 #!/bin/bash -x
 
-test -z ${RBBT_SERVER+x}           && RBBT_SERVER=http://rbbt.bioinfo.cnio.es/ 
+test -z ${RBBT_SERVER+x}           && RBBT_SERVER=http://rbbt.bsc.es/ 
 test -z ${RBBT_FILE_SERVER+x}      && RBBT_FILE_SERVER="$RBBT_SERVER"
 test -z ${RBBT_WORKFLOW_SERVER+x}  && RBBT_WORKFLOW_SERVER="$RBBT_SERVER"
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.35
+  version: 0.1.36
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-10 00:00:00.000000000 Z
+date: 2019-08-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util