Merge branch 'develop'

asdockers-send-to-lrz-dockerhub.sh

@@ -0,0 +1,51 @@
+#!/bin/bash
+
+tools=( sgseq irfinder )
+#tools=( eventpointer asgal )
+#tools=(  mapsplice segemehl star aspli irfinder sgseq spladder whippet asgal eventpointer majiq subjunc minimap hisat gsnap dart crac contextmap bbmap)
+#tools=( star  aspli  irfinder  sgseq spladder whippet asgal eventpointer majiq )
+#unused tools: subjunc bbmap contextmap crac dart gsnap hisat minimap mapsplice segemehl asgal eventpointer majiq
+echo tool-list currently: ${tools[*]}
+
+gitlabimagename="gitlab.lrz.de:5005/ge46ban/dockers/develop/"
+dockerhubimagename="dicastproj/dicast"
+
+
+dockerlist=$(docker images | grep dicast/ | cut -d ' ' -f1)
+
+for i in ${tools[*]}
+do echo tool: $i
+docker tag dicast/$i:0.2 ${gitlabimagename}${i}:0.3
+docker push ${gitlabimagename}${i}:0.3
+done
+
+#docker-compose -f /nfs/proj/AS_dockers/amit/dockers/scripts/snakemake/docker-compose.yml build
+
+for i in ${tools[*]}
+do echo tool: $i
+docker tag dicast/$i:0.2 ${dockerhubimagename}:${i}
+docker push ${dockerhubimagename}:${i}
+done
+
+
+#docker-compose -f /nfs/proj/AS_dockers/amit/dockers/scripts/snakemake/docker-compose.yml build
+
+echo Moving on to delete images
+docker images | grep $gitlabimagename
+docker images | grep $dockerhubimagename
+
+#	echo Countdown ends at 20.
+#for i in $(seq 1 2)
+#do sleep 1
+#echo $i
+#done
+
+	for i in ${tools[*]}
+	do echo tool: $i
+	echo docker rmi ${gitlabimagename}${i}:0.3
+	done
+
+	for i in ${tools[*]}
+	do echo tool: $i
+	echo docker rmi ${dockerhubimagename}:${i}
+	done

docs/build/html/_sources/get-started/setup/snakemake.rst.txt

@@ -9,12 +9,11 @@ Install Snakemake
 
 If you have never worked with conda before you might want to get conda first: https://conda.io/projects/conda/en/latest/user-guide/install/index.html
 
-``Mamba`` is a faster implementation of conda and while optional, is a recommended installation step to support your conda: https://mamba.readthedocs.io/en/latest/installation.html
 
 .. prompt:: bash
 
 	# create conda environment from .yml file with snakemake in it.
-	mamba env create -f scripts/snakemake/dicast-snakemake.yml
+	conda env create -f scripts/snakemake/dicast-snakemake.yml
 
 	# if you want to use DICAST, activate the "dicast-snakemake" environment
 	conda activate dicast-snakemake

docs/build/html/get-started/setup/snakemake.html

@@ -151,13 +151,12 @@
 <h1>Install Snakemake<a class="headerlink" href="#install-snakemake" title="Permalink to this heading"></a></h1>
 <p><code class="docutils literal notranslate"><span class="pre">snakemake</span></code> is the pipe-lining software that enables your DICAST runs. You can set up snakemake in a conda environment.</p>
 <p>If you have never worked with conda before you might want to get conda first: <a class="reference external" href="https://conda.io/projects/conda/en/latest/user-guide/install/index.html">https://conda.io/projects/conda/en/latest/user-guide/install/index.html</a></p>
-<p><code class="docutils literal notranslate"><span class="pre">Mamba</span></code> is a faster implementation of conda and while optional, is a recommended installation step to support your conda: <a class="reference external" href="https://mamba.readthedocs.io/en/latest/installation.html">https://mamba.readthedocs.io/en/latest/installation.html</a></p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><style type="text/css">
 span.prompt1:before {
   content: "$ ";
 }
 </style><span class="prompt1"><span class="c1"># create conda environment from .yml file with snakemake in it.</span></span>
-<span class="prompt1">mamba env create -f scripts/snakemake/dicast-snakemake.yml</span>
+<span class="prompt1">conda env create -f scripts/snakemake/dicast-snakemake.yml</span>
 <span class="prompt1"></span>
 <span class="prompt1"><span class="c1"># if you want to use DICAST, activate the &quot;dicast-snakemake&quot; environment</span></span>
 <span class="prompt1">conda activate dicast-snakemake</span>

docs/source/get-started/setup/snakemake.rst

@@ -9,12 +9,11 @@ Install Snakemake
 
 If you have never worked with conda before you might want to get conda first: https://conda.io/projects/conda/en/latest/user-guide/install/index.html
 
-``Mamba`` is a faster implementation of conda and while optional, is a recommended installation step to support your conda: https://mamba.readthedocs.io/en/latest/installation.html
 
 .. prompt:: bash
 
 	# create conda environment from .yml file with snakemake in it.
-	mamba env create -f scripts/snakemake/dicast-snakemake.yml
+	conda env create -f scripts/snakemake/dicast-snakemake.yml
 
 	# if you want to use DICAST, activate the "dicast-snakemake" environment
 	conda activate dicast-snakemake

scripts/dicast_upset_scripts/compare_plots.py

@@ -15,6 +15,7 @@
 import os 
 import argparse
 import matplotlib
+plt.switch_backend('Agg')
 plt.ioff()