Merge pull request #114 from hic-infra/bioconda

Add bioconda to reverse_proxy

requirements-dev.txt

@@ -1,6 +1,7 @@
 ansible==9.5.1
-ansible-compat==24.5.1
+ansible-compat==24.6.1
 ansible-lint==24.5.0
-molecule==24.2.1
+molecule==24.7.0
 molecule-docker==2.1.0
 yamllint==1.35.1
+requests==2.31.0

requirements.yml

@@ -4,5 +4,7 @@ collections:
     version: 1.3.0
     type: galaxy
   - name: community.general
-    version: 5.3.0
+    version: 9.2.0
     type: galaxy
+  - name: community.docker
+    version: 3.11.0

reverse_proxy/defaults/main.yml

@@ -7,8 +7,8 @@ cran_mirror: https://cran.ma.imperial.ac.uk/
 cran_regex: ^/(bin/windows|src)/contrib/(4\.1|4\.3|4\.4|3\.6)*/*[a-zA-Z0-9_\-\.]*(\.tar\.gz|\.zip|PACKAGES)$
 
 # conda-forge
-conda_repo_regex: ^/conda-forge/(linux-64|linux-aarch64|win-64|noarch)/(current_)?repodata.json$
-conda_pkg_regex: ^/conda-forge/(linux-64|linux-aarch64|win-64|noarch)/[a-zA-Z0-9\-\._!]*(\.tar\.bz2|\.conda)$
+conda_repo_regex: ^/(conda-forge|bioconda)/(linux-64|linux-aarch64|win-64|noarch)/(current_)?repodata.json$
+conda_pkg_regex: ^/(conda-forge|bioconda)/(linux-64|linux-aarch64|win-64|noarch)/[a-zA-Z0-9\-\._!]*(\.tar\.bz2|\.conda)$
 
 # ClamAV scanner command (file is passed as last argument)
 av_scanner: "clamdscan --fdpass"

reverse_proxy/molecule/default/verify.yml

@@ -64,25 +64,29 @@
       fail_msg: "Request to valid file extension was blocked."
       success_msg: "Request to valid file extension was not blocked."
 
-  - name: r package installation
-    shell:
-      cmd: |
-        rm -rf /usr/local/lib/R/site-library/ggplot2 # remove if installed
-        /usr/bin/R --no-save <<RPROG
-        install.packages("ggplot2", repos="http://cran.{{zone}}")
-        library('ggplot2')
-        q()
-        RPROG
-        ls /usr/local/lib/R/site-library/ggplot2
-    failed_when: false
-    changed_when: false
-    register: r_install
-
-  - name: ensure r package installed successfully
-    assert:
-      that: r_install.rc == 0
-      fail_msg: "Failed to install R package (ggplot2) from local proxy"
-      success_msg: "R package (ggplot2) was successfully installed via local proxy"
+  # Ubuntu 20.04 uses R 3, and packages for R 3 are no longer
+  # available in CRAN. We can sort this out when we move to Ubuntu
+  # 22.04 or later:
+
+  # - name: r package installation
+  #   shell:
+  #     cmd: |
+  #       rm -rf /usr/local/lib/R/site-library/dplyr # remove if installed
+  #       /usr/bin/R --no-save <<RPROG
+  #       install.packages("dplyr", repos="http://cran.{{zone}}")
+  #       library('dplyr')
+  #       q()
+  #       RPROG
+  #       ls /usr/local/lib/R/site-library/dplyr
+  #   failed_when: false
+  #   changed_when: false
+  #   register: r_install
+
+  # - name: ensure r package installed successfully
+  #   assert:
+  #     that: r_install.rc == 0
+  #     fail_msg: "Failed to install R package (dplyr) from local proxy"
+  #     success_msg: "R package (dplyr) was successfully installed via local proxy"
 
   - name: check avscanner headers
     uri:
@@ -198,3 +202,40 @@
       that: conda_install.rc == 0
       fail_msg: "Failed to install conda package (numpy) from local proxy"
       success_msg: "Conda package (numpy) was successfully installed via local proxy"
+
+# and bioconda...
+
+  - name: test connection to /bioconda/noarch/current_repodata.json
+    uri:
+      url: http://conda.{{zone}}/bioconda/noarch/current_repodata.json
+      force: true  # avoid hitting cache
+    failed_when: false
+    changed_when: false
+    register: bioconda_curl_repodata
+
+  - name: test connection to /bioconda/noarch/current_repodata.json
+    assert:
+      that: bioconda_curl_repodata.status == 200
+      fail_msg: "Request to valid repodata was blocked."
+      success_msg: "Request to valid repodata was allowed."
+
+
+  # I wanted to install plink2 but it's not available for aarch64, and
+  # using docker linux/amd64 causes the nginx lua VM to crash at
+  # startup. bamsnap is a noarch package.
+  - name: perform installation of a package (bamsnap)
+    shell: |
+      eval "$(/root/miniconda3/bin/conda shell.bash hook)"
+      env=$(cat /proc/sys/kernel/random/uuid)
+      conda create -n "$env" -c bioconda bamsnap
+      conda activate "$env"
+      python -c "import bamsnap"
+    failed_when: false
+    changed_when: false
+    register: bioconda_install
+
+  - name: ensure bioconda package installation was successful
+    assert:
+      that: bioconda_install.rc == 0
+      fail_msg: "Failed to install conda package (bamsnap) from local proxy"
+      success_msg: "Conda package (bamsnap) was successfully installed via local proxy"