Merge pull request #350 from bioinfo-chru-strasbourg/fix_annotation_f…

…ormat_to_table

Fix annotation format to table

.env

@@ -24,7 +24,7 @@ DOCKER_COMPOSE_ENV=.env
 # Docker HOWARD image including HOWARD tool and configuration
 # This image will be build if needed (using Docker HOWARD context)
 #DOCKER_HOWARD_IMAGE=howard:latest
-DOCKER_HOWARD_IMAGE=howard:0.12.1.1
+DOCKER_HOWARD_IMAGE=howard:0.12.2.0
 
 
 ### DOCKER HOWARD CONTEXT

.github/workflows/build.yml

@@ -17,10 +17,10 @@ jobs:
         python-version: [3.10]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -41,7 +41,7 @@ jobs:
         run: cibuildwheel --output-dir wheelhouse
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: wheels
           path: wheelhouse/*.whl
@@ -52,15 +52,15 @@ jobs:
     if: github.event_name == 'push' && github.ref == 'refs/heads/master'
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install twine
 
       - name: Download wheels
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: wheels
           path: wheelhouse

.gitignore

@@ -1,5 +1,6 @@
 __pycache__/
 howard.egg-info/
+howard_ann.egg-info/
 .pytest_cache/
 .cache
 .vscode
@@ -15,10 +16,15 @@ tests/databases/hg19.fa
 tests/databases/hg19.fa.fai
 tests/databases/.DS_Store
 tests/data/TEM*
-tests/*.DS_Store
+tests/.DS_Store
 benchmark
 misc/
 *.DS_Store
 snpEff_*
 .gitignore
-tests/tmp*
+tests/tmp*
+tmp/
+build/
+images/howard/
+images/old/
+kubernetes/

Dockerfile

@@ -1,8 +1,8 @@
 
 ##############################################################
-# Dockerfile Version:   1.7
+# Dockerfile Version:   1.7.1
 # Software:             HOWARD
-# Software Version:     0.12.1.1
+# Software Version:     0.12.2.0
 # Software Website:     https://github.com/bioinfo-chru-strasbourg/howard
 # Licence:              GNU Affero General Public License (AGPL)
 # Description:          HOWARD - Highly Open Workflow for Annotation & Ranking toward genomic variant
@@ -39,12 +39,12 @@
 
 FROM almalinux:8-minimal
 LABEL Software="HOWARD" \
-	Version="0.12.1.1" \
+	Version="0.12.2.0" \
 	Website="https://github.com/bioinfo-chru-strasbourg/howard" \
 	Description="HOWARD" \
 	License="GNU Affero General Public License (AGPL)" \
     maintener="Antony Le Bechec <[email protected]>" \
-	Usage='docker run -v $DATA FOLDER:/data -v $DATABASE_FOLDER:/databases -ti howard:0.12.1.1'
+	Usage='docker run -v $DATA FOLDER:/data -v $DATABASE_FOLDER:/databases -ti howard:0.12.2.0'
 
 
 
@@ -266,7 +266,7 @@ RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
 ###########
 
 ENV TOOL_NAME=howard
-ENV TOOL_VERSION=0.12.1.1
+ENV TOOL_VERSION=0.12.2.0
 ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
 ENV PATH=$DEST/bin:$PATH
 ENV USER_HOME=/root

README.html

@@ -334,9 +334,16 @@ <h2 data-number="2.2" id="python"><span
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="ex">conda</span> activate howard</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> pip install <span class="at">-e</span> .</span>
 <span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="ex">howard</span> <span class="at">--help</span></span></code></pre></div>
-<pre class="text"><code>usage: howard [-h] {query,stats,convert,hgvs,annotation,calculation,prioritization,process,databases,gui} ...
+<pre class="text"><code> _   _  _____        ___    ____  ____
+| | | |/ _ \ \      / / \  |  _ \|  _ \ 
+| |_| | | | \ \ /\ / / _ \ | |_) | | | |
+|  _  | |_| |\ V  V / ___ \|  _ &lt;| |_| |
+|_| |_|\___/  \_/\_/_/   \_\_| \_\____/ 
+
+HOWARD::0.12.2.0 [Antony Le Bechec, Jean-Baptiste Lamouche]
+HOWARD - Highly Open Workflow for Annotation &amp; Ranking toward genomic variant Discovery
 
-HOWARD:0.12.1.1 - Highly Open Workflow for Annotation &amp; Ranking toward genomic variant Discovery
+usage: howard [-h] {query,stats,convert,hgvs,annotation,calculation,prioritization,process,databases,gui} ...
 
 Shared arguments:
   -h, --help            show this help message and exit

README.md

@@ -107,9 +107,16 @@ howard --help
 ```
 
 ``` text
-usage: howard [-h] {query,stats,convert,hgvs,annotation,calculation,prioritization,process,databases,gui} ...
+ _   _  _____        ___    ____  ____
+| | | |/ _ \ \      / / \  |  _ \|  _ \ 
+| |_| | | | \ \ /\ / / _ \ | |_) | | | |
+|  _  | |_| |\ V  V / ___ \|  _ <| |_| |
+|_| |_|\___/  \_/\_/_/   \_\_| \_\____/ 
+                                        
+HOWARD::0.12.2.0 [Antony Le Bechec, Jean-Baptiste Lamouche]
+HOWARD - Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery
 
-HOWARD:0.12.1.1 - Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery
+usage: howard [-h] {query,stats,convert,hgvs,annotation,calculation,prioritization,process,databases,gui} ...
 
 Shared arguments:
   -h, --help            show this help message and exit