Add bioconductor install functionality

README.md

@@ -11,6 +11,8 @@ Set up the latest version of R in Ubuntu systems.
 #### Variables
 
 * `r_cran mirror`: [default: `http://cran.rstudio.com/`]: Your favorite [CRAN mirror](http://cran.r-project.org/mirrors.html)
+* `r_bioclite_url`: [default: `https://bioconductor.org/biocLite.R`]: The `biocLite.R` script URL for [Bioconductor](http://bioconductor.org/) installs
+
 * `r_install_dev`: [default: `false`]: Whether or not install the `r-base-dev` package
 * `r_install`: [default: `[]`]: Additional (apt) packages to install (e.g. `r-recommended`)
 
@@ -20,6 +22,7 @@ Set up the latest version of R in Ubuntu systems.
 * `r_packages`: [default: `[]`]: (CRAN) Packages to install or remove
 * `r_packages.{n}.name`: [required]: The name of the package
 * `r_packages.{n}.state`: [optional, default: `present`]: The state of the package
+* `r_packages.{n}.type`: [optional, default: `cran`]: The type of the package (e.g. `bioconductor`)
 * `r_packages.{n}.lib`: [optional, default: `r_packages_lib`]: The library directory to install the package to
 * `r_packages.{n}.repos`: [optional, default: `r_packages_repos`]: The URL to install the package from
 
@@ -50,9 +53,11 @@ None
     # apt packages
     r_install:
       - r-recommended
-    # cran-r packages
+    # cran or bioconductor (R) packages
     r_packages:
       - name: dplyr
+      - name: Biobase
+        type: bioconductor
 ```
 
 #### License

defaults/main.yml

@@ -1,9 +1,12 @@
 # defaults file for r
 ---
 r_cran_mirror: http://cran.rstudio.com/
+r_bioclite_url: https://bioconductor.org/biocLite.R
+
 r_install_dev: false
 r_install: []
 
+r_packages_type: cran
 r_packages_repos: "{{ r_cran_mirror }}"
 r_packages_lib: /usr/local/lib/R/site-library
 r_packages: []

meta/main.yml

@@ -13,4 +13,7 @@ galaxy_info:
         - trusty
   galaxy_tags:
     - system
+    - r
+    - cran-r
+    - statistics
 dependencies: []

tasks/install.yml

@@ -6,7 +6,7 @@
     state: latest
     update_cache: true
     cache_valid_time: "{{ apt_update_cache_valid_time | default(3600) }}"
-  with_items: r_dependencies
+  with_items: "{{ r_dependencies }}"
   when: "item | trim != ''"
   tags:
     - r-install-dependencies
@@ -15,6 +15,6 @@
   apt:
     name: "{{ item }}"
     state: latest
-  with_items: r_install
+  with_items: "{{ r_install }}"
   tags:
     - r-install-additional

tasks/packages.yml

@@ -14,19 +14,27 @@
       dest: R-remove-package
 
 - name: packages | install
-  command: "R-install-package {{ item.name }}{% if item.lib is defined %} {{ item.lib }}{% endif %}{% if item.repos is defined %} {{ item.repos }}{% endif %}"
+  command: >
+    R-install-package
+      {{ item.name }}
+      {{ item.type | default(r_packages_type) }}
+      {% if item.lib is defined %}{{ item.lib }}{% endif %}
+      {% if item.repos is defined %}{{ item.repos }}{% endif %}
   register: r_install_package
   changed_when: "r_install_package.stdout_lines[-1] is defined and r_install_package.stdout_lines[-1] == 'changed'"
-  with_items: r_packages
+  with_items: "{{ r_packages }}"
   when: item.state is undefined or item.state == 'present'
   tags:
     - r-packages-install
 
 - name: packages | remove
-  command: "R-remove-package {{ item.name }}{% if item.lib is defined %} {{ item.lib }}{% endif %}"
+  command: >
+    R-remove-package
+      {{ item.name }}
+      {% if item.lib is defined %}{{ item.lib }}{% endif %}
   register: r_remove_package
   changed_when: "r_remove_package.stdout_lines[-1] is defined and r_remove_package.stdout_lines[-1] == 'changed'"
-  with_items: r_packages
+  with_items: "{{ r_packages }}"
   when: item.state is defined and item.state == 'absent'
   tags:
     - r-packages-remove

tasks/repository.yml

@@ -13,6 +13,6 @@
     repo: "{{ item.type }} {{ item.url }}"
     state: present
     update_cache: true
-  with_items: r_repository
+  with_items: "{{ r_repository }}"
   tags:
     - r-repository-add

templates/usr/local/bin/R-install-package.j2

@@ -1,16 +1,27 @@
 #!/usr/bin/env r
 
 if (is.null(argv) | length(argv) < 1) {
-  cat("Usage: R-install-package package [lib] [repos]\n");
+  cat("Usage: R-install-package package [type] [lib] [repos]\n");
   q(status = 1);
 }
 
 package = argv[1]
-lib = ifelse(is.na(argv[2]), '{{ r_packages_lib }}', argv[2]);
-repos = ifelse(is.na(argv[3]), '{{ r_packages_repos }}', argv[3]);
+type = ifelse(is.na(argv[2]), '{{ r_packages_type }}', argv[2]);
+lib = ifelse(is.na(argv[3]), '{{ r_packages_lib }}', argv[3]);
 
-if (!(package %in% installed.packages(lib.loc = lib)[,'Package'])) {
-  withCallingHandlers(install.packages(package, lib, repos), warning = stop);
+if (!(package %in% installed.packages(lib.loc = lib)[, 'Package'])) {
+  if (type == "cran") {
+    repos = ifelse(is.na(argv[4]), '{{ r_packages_repos }}', argv[4]);
+    withCallingHandlers(install.packages(package, lib, repos), warning = stop);
+  } else if (type == "bioconductor") {
+    withCallingHandlers({
+      source("{{ r_bioclite_url }}");
+      biocLite(package, lib=lib, suppressUpdates=TRUE, suppressAutoUpdate=TRUE, ask=FALSE);
+    }, warning = stop)
+  } else {
+    cat("Unrecognised type\n");
+    q(status = 1);
+  }
   cat("changed\n");
 } else {
   cat("unchanged\n");

tests/test.retry

@@ -0,0 +1 @@
+localhost

tests/test.yml

@@ -18,3 +18,6 @@
 
       - name: foreign
         state: absent
+
+      - name: Biobase
+        type: bioconductor

vars/main.yml

@@ -3,6 +3,7 @@
 r_repository:
   - type: deb
     url: "{{ r_cran_mirror }}/bin/linux/ubuntu {{ ansible_distribution_release }}/"
+
 r_dependencies:
   - r-base
   - littler