Merge branch 'dev' of ssh://git-r3lab-server.uni.lu:8022/shaman.narayanasamy/IMP into dev

docker/Dockerfile

@@ -154,17 +154,22 @@ RUN cd /home/imp/tmp \
     && ./configure \
     && make \
     && make install \
-    && cd .. && rm -rf parallel* \
+    && cd .. && rm -rf parallel*
+
 ## sortmerna
+RUN cd /home/imp/tmp \
     && wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/sortmerna.2.0.tgz \
     && tar -xzf sortmerna.2.0.tgz \
     && cd sortmerna-2.0 \
     && sh build.sh \
     && mv sortmerna indexdb_rna /usr/bin/. \
     && mv scripts/*.sh /home/imp/lib/. \
-    && cd .. && rm -rf sortmerna* \
+    && cd .. && rm -rf sortmerna*
 ## bedtools2
-    && git clone https://git-r3lab.uni.lu/R3/bedtools2.git \
+RUN cd /home/imp/tmp \
+    && git config --global http.postBuffer 2M \
+    && git config --global http.maxRequestBuffer 100M \
+    && GIT_CURL_VERBOSE=1 git clone https://git-r3lab.uni.lu/R3/bedtools2.git \
     && cd bedtools2 \
     && git checkout v2.22.0 \
     && make
@@ -210,10 +215,12 @@ RUN cd /home/imp/lib
 
 ## Quast/metaQuast
 RUN cd /home/imp/lib \
-    && git clone https://github.com/ablab/quast.git \
-    && cd quast \
-    && git checkout release_3.1 \
-    && ./metaquast.py --test-no-ref \
+    && git config --global http.postBuffer 2M \
+    && git config --global http.maxRequestBuffer 100M \
+    && git config --global core.compression 0 \
+    && wget https://github.com/ablab/quast/archive/release_3.1.zip -O quast.zip \
+    && unzip quast.zip \
+    && cd quast-release_3.1 \
     && ln -s $PWD/metaquast.py /usr/bin/metaquast
 
 ######################

init.rule

@@ -34,6 +34,13 @@ rule _DOWNLOAD_HUMAN_DB:
         rm -rf $TMPD
         """
 
+rule _INIT_QUAST:
+    output:
+        ""
+    shell:
+        """
+        metaquast --test-no-ref
+        """
 
 rule _DOWNLOAD_SORTMERNA_DATABASES:
     output:

lib/imp.js

@@ -253,12 +253,11 @@ $('#but-variant').on('change', function(){
 
 // set last tab in cookie
 $('#tabs a[data-toggle="tab"]').on('shown.bs.tab', function (e) {
-  Cookies.set('tab', '#' + e.target.id);
-  e.target
+  $.cookie('tab', $(e.target).attr('href'));
 })
 // show lat iopenned tab or first one
-if(Cookie.get('tab')){
-    $(Cookie.get('tab')).tab('show');
+if($.cookie('tab')){
+    $('#tabs li > a[href=' + $.cookie('tab') + ']').tab('show')
 } else {
     $('#tabs li:first > a').tab('show');
 }

rules/Util.rules

@@ -42,7 +42,6 @@ rule REPORT:
             "lib/bootstrap.min.css",
             "lib/bootstrap.min.js",
             "lib/imp.js",
-
         ] +
         expand(["{dir}/workflow.png", "{dir}/workflow.pdf"], dir=OUTPUTDIR)
     output:
@@ -56,7 +55,12 @@ rule REPORT:
             towrite = json.dumps(config)
             whandle.write("IMP_CONFIG = %s;" % towrite)
         shell("cp {input[0]} {params.outdir}/REPORT.html")
-        shell("cp {input[1:]} {params.outdir}")
+        shell("cp -f {input[1]} {params.outdir}")
+        shell("cp -f {input[2]} {params.outdir}")
+        shell("cp -f {input[3]} {params.outdir}")
+        shell("cp -f {input[4]} {params.outdir}")
+        shell("cp -f {input[5]} {params.outdir}")
+        shell("cp -f {input[6]} {params.outdir}")
 
 
 rule REPORT2: