diff --git a/docker/Dockerfile b/docker/Dockerfile index 4a2b5544dc9b47ea8cf6bd17bdff0d509da083ee..927ae7e651e9cf4f79ff4fb76352612283a954e5 100644 --- a/docker/Dockerfile +++ b/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 ###################### diff --git a/init.rule b/init.rule index 950a09aa739be75265af5c24173467c7332a4638..02fa6282c55138a48050812557d2cab882003f2b 100644 --- a/init.rule +++ b/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: diff --git a/lib/imp.js b/lib/imp.js index 05c901959f74d8e923e9a65f6ef0a84a38d90d52..885f8f956fb154ae1f26a946005671560a9aea55 100644 --- a/lib/imp.js +++ b/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'); } diff --git a/rules/Util.rules b/rules/Util.rules index 2d3d291a3765c114f2445ea71a46ec99fb50ad35..25049e18eb22fb1a41095036e48cb6b3262f63af 100644 --- a/rules/Util.rules +++ b/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: