rbbt-image 0.1.35 → 0.1.36

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (8) hide show
  1. checksums.yaml +4 -4
  2. data/bin/build_rbbt_provision_sh.rb +3 -3
  3. data/share/provision_scripts/R_setup.sh +3 -4
  4. data/share/provision_scripts/python_setup.sh +9 -8
  5. data/share/provision_scripts/ruby_setup.sh +0 -1
  6. data/share/provision_scripts/ubuntu_setup.sh +70 -5
  7. data/share/provision_scripts/variables.sh +1 -1
  8. metadata +2 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA256:
3
- metadata.gz: c7c7d21c1945100f43485cec703a2af72e181e7d91589395e08e1cb07d430a93
4
- data.tar.gz: 06d21330a2d93254ac61ca1f7cc8432790b2ab914bd69c7f0c40044288db5adf
3
+ metadata.gz: b6ed0fbc0b9b6ea6d4f6b7f1cd9931bebd8e5438ec37b5c73ecdaf545ffde7b2
4
+ data.tar.gz: 68e3073a6bd603fa0404fb3403ecf87c22c0731546b24afc4e2ea059b73a2acf
5
5
  SHA512:
6
- metadata.gz: 7f6b918673bb5c735679713a1a2d689925580d642859782b828063776a6817266c1f372be5641f8a93da7058f83da5a1e455164a4ad104aa32842ce0d456a2f9
7
- data.tar.gz: 6015203a7fb0abf5fb4145998c1acd87c2b7cdb957d94f27bf1bbdcebacd02ee4c5c1cf38dd3012653e6e878a98ba126954fdabdfae4d54f37ec63c4e04d91ef
6
+ metadata.gz: 288e7e36fed3c08d32416a88af59caffe684d5fdefdf22b5a9b5e1ea051f825c3b1e138932d787d797ff8aa142ff2d5b8a5d1481a28f6f4ca5388df956f231e8
7
+ data.tar.gz: 5910cee842328c52a9057b85184aaba2149d6d8427efd4e164448af75651ca2783a881e612b6517baba7dce920a3389236a04d1bc45b17bac9ff0770a0d6fcda
data/bin/build_rbbt_provision_sh.rb CHANGED
@@ -119,9 +119,6 @@ else
119
119
  end
120
120
  }
121
121
 
122
- echo "[ -f ~/.rbbt/etc/environment ] && . ~/.rbbt/etc/environment" >> "/etc/rbbt_environment"
123
- echo "source /etc/rbbt_environment" >> /etc/profile
124
-
125
122
  #{
126
123
  if not SKIP_BASE_SYSTEM and R_CUSTOM
127
124
  "echo 1.1 Setting custom R"
@@ -182,6 +179,9 @@ else
182
179
  "echo SKIPPED\necho"
183
180
  end
184
181
  }
182
+
183
+ echo "[ -f ~/.rbbt/etc/environment ] && . ~/.rbbt/etc/environment" >> "/etc/rbbt_environment"
184
+ echo "source /etc/rbbt_environment" >> /etc/profile
185
185
  EOF
186
186
 
187
187
  provision_script +=<<-EOF
data/share/provision_scripts/R_setup.sh CHANGED
@@ -15,9 +15,8 @@ cd R-*/
15
15
  make && make install
16
16
 
17
17
  echo "# For RSRuby gem " >> /etc/rbbt_environment
18
- echo "export R_HOME='/usr/local/lib/R'" >> /etc/rbbt_environment
19
- echo "export PATH=\"$R_HOME/bin:$PATH\"" >> /etc/rbbt_environment
20
- echo "export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:\$R_HOME/lib\"" >> /etc/rbbt_environment
21
- echo "export LD_RUN_PATH=\"\$LD_RUN_PATH:\$R_HOME/lib\"" >> /etc/rbbt_environment
18
+ echo 'export R_HOME="/usr/local/lib/R"' >> /etc/rbbt_environment
19
+ echo '_add_path "$R_HOME/bin/" # Rserver' >> /etc/rbbt_environment
20
+ echo '_add_lib_path "$R_HOME/lib/" # Rserver' >> /etc/rbbt_environment
22
21
 
23
22
  . /etc/rbbt_environment
data/share/provision_scripts/python_setup.sh CHANGED
@@ -1,15 +1,16 @@
1
1
  wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" -O /tmp/miniconda.sh
2
- bash /tmp/miniconda.sh -b -p /opt/miniconda3
2
+ echo "# Python conda " >> /etc/rbbt_environment
3
3
 
4
- [ -d /opt/bin/conda ] || mkdir -p /opt/bin/conda
5
- ln -s /opt/miniconda3/bin/conda /opt/bin/conda
4
+ bash /tmp/miniconda.sh -b -p /usr/local/miniconda3
5
+ ln -s /usr/local/miniconda3/bin/conda /usr/local/bin/conda
6
+ echo '_add_path "/usr/local/miniconda3/bin/"' >> /etc/rbbt_environment
6
7
 
7
- conda create --yes -n python3 python=3.6.1 pip
8
- rm -Rf /opt/miniconda3/pkgs
9
8
  conda create --yes -n python2 python=2.7 pip
10
- rm -Rf /opt/miniconda3/pkgs
11
9
 
12
- echo "# Python conda " >> /etc/rbbt_environment
13
- echo 'export PATH="/opt/bin/:/opt/miniconda3/envs/python3/bin/:$PATH"' >> /etc/rbbt_environment
10
+ conda create --yes -n python3 python=3 pip
11
+
12
+ echo '_add_path "/usr/local/miniconda3/envs/python2/bin/"' >> /etc/rbbt_environment
13
+ echo '_add_path "/usr/local/miniconda3/envs/python3/bin/"' >> /etc/rbbt_environment
14
14
 
15
+ rm -Rf /usr/local/miniconda3/pkgs
15
16
  source /etc/rbbt_environment
data/share/provision_scripts/ruby_setup.sh CHANGED
@@ -13,7 +13,6 @@ make && make install
13
13
 
14
14
  unset _small_version
15
15
 
16
- echo 'export PATH="/usr/local/bin:/opt/bin:$PATH" #Ruby2' >> /etc/rbbt_environment
17
16
  . /etc/rbbt_environment
18
17
 
19
18
  #\curl -sSL https://get.rvm.io | bash -s stable
data/share/provision_scripts/ubuntu_setup.sh CHANGED
@@ -3,6 +3,68 @@
3
3
  # INSTALL
4
4
  # =======
5
5
 
6
+ cat << 'EOF' > /etc/rbbt_environment
7
+ _var_content(){
8
+ var=$1
9
+ eval echo "$"$(echo $var)
10
+ }
11
+
12
+ _append_with_colon(){
13
+ var=$1
14
+ value=$2
15
+
16
+ current=`_var_content $var`
17
+
18
+ if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" &> /dev/null; then
19
+ eval $(echo $var)="\"$current:$value\""
20
+ fi
21
+ }
22
+
23
+ _append_with_space(){
24
+ var=$1
25
+ value=$2
26
+
27
+ current=`_var_content $var`
28
+
29
+ if ! echo $current | grep "\(^\| \)$value\( \|$\)" &> /dev/null; then
30
+ eval $(echo $var)="\"$current:$value\""
31
+ fi
32
+ }
33
+
34
+ _prepend_with_colon(){
35
+ var=$1
36
+ value=$2
37
+
38
+ current=`_var_content $var`
39
+
40
+ if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" &> /dev/null; then
41
+ eval $(echo $var)="\"$value:$current\""
42
+ fi
43
+ }
44
+
45
+ _prepend_with_space(){
46
+ var=$1
47
+ value=$2
48
+
49
+ current=`_var_content $var`
50
+
51
+ if ! echo $current | grep "\(^\| \)$value\( \|$\)" &> /dev/null; then
52
+ eval $(echo $var)="\"$value $current\""
53
+ fi
54
+ }
55
+
56
+ _add_path(){
57
+ _prepend_with_colon PATH "$1"
58
+ }
59
+
60
+ _add_libpath(){
61
+ _prepend_with_colon LD_LIBRARY_PATH "$1"
62
+ _prepend_with_colon LD_RUN_PATH "$1"
63
+ }
64
+ EOF
65
+
66
+ . /etc/rbbt_environment
67
+
6
68
  # Basic system requirements
7
69
  # -------------------------
8
70
  apt-get -y update
@@ -22,7 +84,7 @@ apt-get -y install \
22
84
  tcsh gawk \
23
85
  libtbb-dev
24
86
 
25
- add-apt-repository ppa:george-edison55/cmake-3.x
87
+ #add-apt-repository ppa:george-edison55/cmake-3.x
26
88
  apt-get -y update
27
89
  apt-get -y update
28
90
  apt-get -y install cmake
@@ -36,12 +98,15 @@ rm /usr/lib/R/bin/Rserve
36
98
  ln -s /usr/lib/R/site-library/Rserve/libs/Rserve /usr/lib/R/bin/Rserve
37
99
 
38
100
  echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/rbbt_environment
39
- echo 'export PATH="$R_HOME/bin/:$PATH" # Rserver' >> /etc/rbbt_environment
101
+ echo '_add_path "$R_HOME/bin/" # Rserver' >> /etc/rbbt_environment
102
+
103
+ [ -d /opt/bin ] || mkdir -p /opt/bin
104
+ echo '_add_path "/opt/bin/"' >> /etc/rbbt_environment
105
+
106
+ [ -d /usr/local/bin ] || mkdir -p /usr/local/bin
107
+ echo '_add_path "/usr/local/bin/"' >> /etc/rbbt_environment
40
108
 
41
109
  . /etc/rbbt_environment
42
110
 
43
111
  apt-get clean
44
112
  rm -rf /var/lib/apt/lists/*
45
-
46
-
47
-
data/share/provision_scripts/variables.sh CHANGED
@@ -1,6 +1,6 @@
1
1
  #!/bin/bash -x
2
2
 
3
- test -z ${RBBT_SERVER+x} && RBBT_SERVER=http://rbbt.bioinfo.cnio.es/
3
+ test -z ${RBBT_SERVER+x} && RBBT_SERVER=http://rbbt.bsc.es/
4
4
  test -z ${RBBT_FILE_SERVER+x} && RBBT_FILE_SERVER="$RBBT_SERVER"
5
5
  test -z ${RBBT_WORKFLOW_SERVER+x} && RBBT_WORKFLOW_SERVER="$RBBT_SERVER"
6
6
 
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbbt-image
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.1.35
4
+ version: 0.1.36
5
5
  platform: ruby
6
6
  authors:
7
7
  - Miguel Vazquez
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2019-07-10 00:00:00.000000000 Z
11
+ date: 2019-08-07 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rbbt-util