Merge branch 'development' into master

.github/workflows/main.yml

@@ -2,24 +2,21 @@ name: CI
 
 on:
   push:
-    branches: [ development ]
+    branches:
+      - development
+      - master
   pull_request:
-    branches: [ development ]
+    branches:
+      - development
+      - master
 
-
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
   build:
-    # The type of runner that the job will run on
     runs-on: ubuntu-latest
 
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout
         uses: actions/checkout@v2
 
@@ -43,7 +40,7 @@ jobs:
           name: mosca
           path: /tmp/mosca.tar
 
-  use:
+  mgmt-workflow:
     runs-on: ubuntu-latest
     needs: build
     steps:
@@ -61,31 +58,31 @@ jobs:
           docker load --input /tmp/mosca.tar
           docker image ls -a
 
-      - name: Check base entrypoint
-        run: docker run mosca /bin/bash -c "ls"
+      - name: MGMT workflow
+        run: docker run mosca /bin/bash -c "mosca -c MOSCARDO/configs/mgmt_config.json"
+
+  mgmp-workflow:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Download artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: mosca
+          path: /tmp
+
+      - name: Load Docker image
+        run: |
+          docker load --input /tmp/mosca.tar
+          docker image ls -a
 
       - name: Create named volume
         run: docker volume create named_volume
 
-      - name: MGMT workflow
-        run: docker run mosca /bin/bash -c "mosca.py -c MOSCARDO/configs/mgmt_config.json; rm -r output"
-
-      - name: test_docker
+      - name: MGMP workflow
         run: >
-          docker run -v named_volume:/data -v /var/run/docker.sock:/var/run/docker.sock mosca /bin/bash 
-          -c 'cp MOSCARDO/input/mp1/mp1.RAW data/mp1.RAW; docker run --rm -e WINEDEBUG=-all -v named_volume:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/mp1.RAW --mgf --filter "peakPicking cwt"; ls /data'
-
-      #- name: MGMP workflow
-      #  run: >
-      #    docker run -v named_volume:/data -v /var/run/docker.sock:/var/run/docker.sock mosca /bin/bash
-      #    -c "mosca.py -c MOSCARDO/configs/mgmp_config.json"
-
-      #- name: MG only workflow
-      #  run: >
-      #    docker run mosca /bin/bash -c "mkdir resources_directory; mv MOSCARDO/data/cdd.tar.gz resources_directory;
-      #    cp MOSCARDO/data/mg_R1.fastq.gz MOSCARDO/data/mg_R1_001.fastq.gz;
-      #    cp MOSCARDO/data/mg_R2.fastq.gz MOSCARDO/data/mg_R2_001.fastq.gz;
-      #    mosca.py -c MOSCARDO/configs/mg_only_config.json"
-
-      #- name: MT only workflow
-      #  run: docker run mosca /bin/bash -c "mosca.py -c MOSCARDO/configs/mt_config.json"
+          docker run -v named_volume:/data -v /var/run/docker.sock:/var/run/docker.sock mosca /bin/bash
+          -c "mosca -c MOSCARDO/configs/mgmp_config.json; du -sh output/*; df -h"

Dockerfile_CI

@@ -1,3 +1,7 @@
+# This Dockerfile should only be used for testing purposes
+# It differs from the main Dockerfile by including the download of MOSCARDO's files to be run with MOSCA
+# Also includes the creation of a named_volume automatically, neccessary for MP spectra conversion
+
 FROM continuumio/miniconda3
 
 VOLUME ["named_volume"]
@@ -13,8 +17,13 @@ RUN buildDeps='build-essential zlib1g-dev' \
 # Install MOSCA
 && git clone https://github.com/iquasere/MOSCA.git -b development \
 && bash MOSCA/install.bash --mosca_env "$(conda info --base)" \
+# Fix AttributeError: module 'lib' has no attribute 'X509_V_FLAG_CB_ISSUER_CHECK' \
+# https://stackoverflow.com/questions/74981558/error-updating-python3-pip-attributeerror-module-lib-has-no-attribute-openss
+# https://stackoverflow.com/questions/73830524/attributeerror-module-lib-has-no-attribute-x509-v-flag-cb-issuer-check
+&& pip install cryptography==38.0.4 \
+&& pip install pyopenssl --upgrade \
 && conda clean --all \
-&& apt-get install -y packagekit-gtk3-module libasound2 libdbus-glib-1-2 libx11-xcb1 curl \
+&& apt-get install -y curl \
 && curl -fsSL https://get.docker.com -o get-docker.sh \
 && sh get-docker.sh \
 && apt-get purge -y --auto-remove $buildDeps

README.md

@@ -4,7 +4,7 @@
   <img width="40%" src="resources/mosca_logo.png" alt="Logo" title="Logo by Sérgio A. Silva">
 </p>
 
-[![Development CI](https://github.com/iquasere/MOSCA/actions/workflows/main.yml/badge.svg?branch=development)](
+[![Development CI](https://github.com/iquasere/MOSCA/actions/workflows/main.yml/badge.svg)](
 https://github.com/iquasere/MOSCA/actions/workflows/main.yml) [
 ![GitHub release](https://img.shields.io/github/release/iquasere/MOSCA.svg)](
 https://github.com/iquasere/MOSCA/releases/latest) [

base_environment.yml

@@ -6,6 +6,4 @@ channels:
   - defaults
 dependencies:
   - python >=3.9
-  - pandas
-  - snakemake-minimal
-  - mamba
+  - snakemake

build.sh

@@ -1,7 +1,5 @@
-dir="${PREFIX}/share/MOSCA"
-mkdir -p "${dir}/scripts" "${PREFIX}/bin"
-cp workflow/scripts/* "${dir}/scripts"
-cp workflow/Snakefile workflow/mosca.py "${dir}/scripts"
-cp -r resources "${dir}/resources"
-chmod +x "${dir}/scripts/mosca.py"
-ln -s "${dir}/scripts/mosca.py" "${PREFIX}/bin/"
+echo "Storing MOSCA's files in the Conda environment at: ${PREFIX}"
+mkdir -p "${PREFIX}/share/MOSCA" "${PREFIX}/bin"
+cp -r MOSCA/workflow/* "${PREFIX}/share/MOSCA"
+chmod +x "${PREFIX}/share/MOSCA/mosca.py"
+ln -s "${PREFIX}/share/MOSCA/mosca.py" "${PREFIX}/bin/mosca"