{"id":634,"date":"2016-05-31T14:20:03","date_gmt":"2016-05-31T12:20:03","guid":{"rendered":"http:\/\/vm-bioinfo-wp.toulouse.inra.fr\/?page_id=634"},"modified":"2020-07-29T10:45:58","modified_gmt":"2020-07-29T08:45:58","slug":"software_faq","status":"publish","type":"page","link":"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/faq\/software_faq\/","title":{"rendered":"Software"},"content":{"rendered":"<h6>SLURM Cluster<\/h6>\n\t\t\t\t\t\t<style>\r\n\t\t\t\t\t#wpsm_accordion_2590 .wpsm_panel-heading{\r\npadding:0px !important;\r\n}\r\n#wpsm_accordion_2590 .wpsm_panel-title {\r\nmargin:0px !important; \r\ntext-transform:none !important;\r\nline-height: 1 !important;\r\n}\r\n#wpsm_accordion_2590 .wpsm_panel-title a{\r\ntext-decoration:none;\r\ncolor:#000000 !important;\r\nfont-size:14px !important;\r\ndisplay:block;\r\npadding:0px;\r\nfont-family: Sans !important;\r\npadding-top: 10px;\r\npadding-bottom: 10px;\r\nborder-bottom:1px solid  #ddd !important;\r\n\r\n}\r\n#wpsm_accordion_2590 .wpsm_panel-title a:hover,#wpsm_accordion_2590 .wpsm_panel-title a:visited, #wpsm_accordion_2590 .wpsm_panel-title a:focus {\r\n\tcolor:#000000 !important;\r\n}\r\n#wpsm_accordion_2590 .acc-a{\r\n\tcolor: #000000 !important;\r\n\tbackground-color:#ffffff !important;\r\n\tborder-color: #ddd;\r\n}\r\n#wpsm_accordion_2590 .wpsm_panel-default > .wpsm_panel-heading{\r\n\tcolor: #000000 !important;\r\n\tbackground-color: #ffffff !important;\r\n\tborder-color: #ffffff !important;\r\n\tborder-top-left-radius: 0px;\r\n\tborder-top-right-radius: 0px;\r\n}\r\n#wpsm_accordion_2590 .wpsm_panel-default {\r\n\t\r\n\tborder:1px solid transparent !important;\r\n\r\n\t}\r\n#wpsm_accordion_2590 {\r\n\tmargin-bottom: 20px;\r\n\toverflow: hidden;\r\n\tfloat: left;\r\n\twidth: 100%;\r\n\tdisplay: block;\r\n}\r\n#wpsm_accordion_2590 .ac_title_class{\r\n\tdisplay: inline-block;\r\n    padding-top: 5px;\r\n    padding-bottom: 5px;\r\n    padding-left: 13px;\r\n    padding-right: 10px;\r\n    border: 0px solid #ddd;\r\n\tfont-size:14px !important;\r\nfont-family: Sans !important;\r\n\t\r\n\r\n}\r\n#wpsm_accordion_2590  .wpsm_panel {\r\n\toverflow:hidden;\r\n\t-webkit-box-shadow: 0 0px 0px rgba(0, 0, 0, .05);\r\n\tbox-shadow: 0 0px 0px rgba(0, 0, 0, .05);\r\n\t\r\n\t\tborder-radius: 4px;\r\n\t}\r\n#wpsm_accordion_2590  .wpsm_panel + .wpsm_panel {\r\n\t\tmargin-top: 5px;\r\n\t}\r\n#wpsm_accordion_2590  .wpsm_panel-body{\r\nbackground-color:#ffffff !important;\r\ncolor:#000000 !important;\r\nborder-top-color: #ffffff !important;\r\nfont-size:12px !important;\r\nfont-family: Sans !important;\r\noverflow: hidden;\r\n\r\nborder: 0px solid #ddd !important;\r\n\r\nborder-top:0px !important;\r\npadding-left: 60px;\r\n}\r\n\r\n#wpsm_accordion_2590 .ac_open_cl_icon{\r\n\tbackground-color:#ffffff;\r\n\tcolor: #ba195c;\r\n\t\r\n     padding-top: 5px; \r\n     padding-bottom: 5px; \r\n\t margin-left:10px;\r\n    line-height: 1.0;\r\n    font-size:14px !important;\r\ntext-align: center !important;\r\n     width: 32px !important;\r\n    display: inline-block;\r\n\t\r\n\t\r\n}\r\n#wpsm_accordion_2590 .ac_open_cl_number{\r\n width: 25px !important;\r\n    display: inline-block;\r\n\t margin-left:10px;\r\n\t text-align: center !important;\r\n\t font-size:14px !important;\r\n\r\n}\r\n\r\n\t\t\t\r\n\t\t\t\t\r\n.entry h4 span {\r\n\r\ncolor: #ba195c;\r\n\r\n}\t\t\t\t\t\r\n\t\t\t<\/style>\r\n\t\t\t<div class=\"wpsm_panel-group\" id=\"wpsm_accordion_2590\" >\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse1\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tIs a software is already installed on the cluster?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse1\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<ul>\r\n\t<li>On our Web site (Resources):\u00a0<a class=\"internal-link\" href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/resources\/softwares\/\">Software<\/a><\/li>\r\n\t<li>On genologin with alias command \"search_module\" (case insensitive):<\/li>\r\n<\/ul>\r\n<p><code>search_module <\/code><code><em>soft_name (or part of soft_name)<\/em><\/code><\/p>\r\n<ul>\r\n\t<li>On genologin server with \" ls\" command:<\/li>\r\n<\/ul>\r\n<p><code>ls \/usr\/local\/bioinfo\/src|grep -i\u00a0<em>soft_name<\/em><\/code><\/p>\r\n<ul>\r\n\t<li>On genologin server with \"module\" command:<\/li>\r\n<\/ul>\r\n<p><code>module avail<\/code>\u00a0: display all available software installed on the cluster<\/p>\r\n<p><code>module avail <em>category\/soft_name<\/em><\/code>\u00a0: display available versions for a specific application (with category in bioinfo,compiler,mpi or system) (case sensitive)<\/p>\r\n<p><code>module avail -t 2>&1 | grep -i <em>soft_name<\/em><\/code>\u00a0:\u00a0display available versions for a specific application<\/p>\r\n<p><strong>Examples :<\/strong><\/p>\r\n<p><code>$ search_module blast<\/code><br \/>\r\n<code>bioinfo\/blast-2.2.26<\/code><br \/>\r\n<code>bioinfo\/ncbi-blast-2.2.29+<\/code><br \/>\r\n<code>bioinfo\/ncbi-blast-2.6.0+<\/code><br \/>\r\n<code>bioinfo\/RMBlast-2.6.0<\/code><br \/>\r\n<code>bioinfo\/samblaster-v.0.1.24<\/code><br \/>\r\n<code>bioinfo\/WuBlast2.0<\/code><\/p>\r\n<p>\u00a0<\/p>\r\n<p><code>$ module avail bioinfo\/cutadapt<\/code><\/p>\r\n<p><code>$-------------\/tools\/share\/Modules ----------------------------------------<br \/>\r\nbioinfo\/cutadapt-1.14-python-2.7.2 bioinfo\/cutadapt-1.14-python-3.4.3<\/code><\/p>\r\n<p>\u00a0<\/p>\r\n<p><code>$ module avail -t 2>&1 | grep -i openmpi<\/code><br \/>\r\n<code>mpi\/openmpi-1.6.5<\/code><br \/>\r\n<code>mpi\/openmpi-1.8.1<\/code><br \/>\r\n<code>mpi\/openmpi-1.8.8<\/code><br \/>\r\n<code>mpi\/openmpi-1.8.8-intel2018.0.128<\/code><br \/>\r\n<code>mpi\/openmpi-2.1.2<\/code><br \/>\r\n<code>mpi\/openmpi-2.1.2-intel2018.0.128<\/code><\/p>\r\n<p>\u00a0<\/p>\r\n<p><strong>Find Python package:<\/strong><\/p>\r\n<p>On genologin.toulouse.inra.fr server with alias command \"search_Python_package\" (case insentitive):<\/p>\r\n<p><code>search_Python_package <em>package_name<\/em><\/code><\/p>\r\n<p><strong>Find R package:<\/strong><\/p>\r\n<p>On genologin.toulouse.inra.fr server with alias command \"search_R_package\" (case sensitive):<\/p>\r\n<p><code>search_R_package <em>package_name<\/em><\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse2\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tWhere are installed software on Slurm\/Genologin cluster?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse2\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<ul>\r\n\t<li><strong>Bioinfo software:<\/strong> \/usr\/local\/bioinfo\/src\/<\/li>\r\n\t<li><strong>Others tools and libraries:<\/strong> \/tools\/<\/li>\r\n\t<li><strong>Compilers:<\/strong> \/tools\/compilers<\/li>\r\n<\/ul>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse3\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tAsk for a software installation on Slurm\/Genologin cluster\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse3\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Software installation or update are performed by complete the following form: <a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/help\/install-soft\/\">Software installation<\/a><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse4\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tRun a software\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse4\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<ul>\r\n\t<li><strong>Run a specific application<\/strong><\/li>\r\n<\/ul>\r\n<p>We\u00a0 now use <a href=\"http:\/\/modules.sourceforge.net\/\" target=\"_blank\" rel=\"noopener\">Environment Modules<\/a> to dynamically set up environments for different applications (see \"How to use module command ?\" section of this FAQ for more information).<\/p>\r\n<p>To run a software you need to load <span id=\"result_box\" class=\"short_text\" lang=\"en\"><span class=\"\">\u00a0the corresponding module.<\/span><\/span><\/p>\r\n<p><strong>Examples:<\/strong><\/p>\r\n<p>To use blast:<\/p>\r\n<p>$\u00a0<code>module load bioinfo\/blast-2.2.26<\/code><\/p>\r\n<p>To verify:<\/p>\r\n<p><code>$ which blastall<\/code><br \/>\r\n <code>\/usr\/local\/bioinfo\/src\/NCBI_Blast\/blast-2.2.26\/bin\/blastall<\/code><\/p>\r\n<p>To use Python 2.7.2<\/p>\r\n<p><code>$ module load system\/Python-2.7.2<\/code><br \/>\r\n <code>$ which python<\/code><br \/>\r\n <code>\/tools\/python\/2.7.2\/bin\/python<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse5\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHelp to run a software\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse5\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<ul>\r\n\t<li><strong>Software documentation<\/strong><\/li>\r\n<\/ul>\r\n<p>Typically , documentation is provided by the soft in the installation folder (\/usr\/local\/bioinfo\/src\/soft_name) and on the <strong>web site of the software<\/strong> (we give the link to the website of each software on the <a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/resources-2\/softwares\/\">Software page<\/a>).<\/p>\r\n<ul>\r\n\t<li><strong>Use on SLURM cluster<\/strong><\/li>\r\n<\/ul>\r\n<p>You can also find specific information in a \"How_to_use_SLURM_soft_name\" file in the software installation directory (\/usr\/local\/bioinfo\/src\/soft_name) or on our web site <a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/resources-2\/softwares\/\">Software page<\/a>\u00a0 (Avaibility\/Use column, click on SLURM cluster link) .<\/p>\r\n<ul>\r\n\t<li><strong>Example directory<\/strong><\/li>\r\n<\/ul>\r\n<p>In the software installation directory, there is often a basic example submission job in an \"example_on_cluster\" directory (you need to copy it in your work space to run it to test, otherwise you'll have permission issues).\u00a0<\/p>\r\n<p>Example with bowtie:<\/p>\r\n<p><code>$ ls -1 \/usr\/local\/bioinfo\/src\/bowtie\/<\/code><br \/>\r\n<code> bowtie-1.2.1.1<\/code><br \/>\r\n<code> bowtie-1.2.1.1-linux-x86_64.zip<\/code><br \/>\r\n<code> bowtie2-2.2.9<\/code><br \/>\r\n<code> bowtie2-2.3.3.1<\/code><br \/>\r\n<code> bowtie2-2.3.3.1-linux-x86_64.zip<\/code><br \/>\r\n<code> example_on_cluster<\/code><br \/>\r\n<code> How_to_use_SLURM_bowtie<\/code><\/p>\r\n<p><code>$ ls -1 \/usr\/local\/bioinfo\/src\/bowtie\/example_on_cluster\/<\/code><br \/>\r\n<code> errot.txt<\/code><br \/>\r\n<code> example<\/code><br \/>\r\n<code> lambda_virus.1.bt2<\/code><br \/>\r\n<code> lambda_virus.2.bt2<\/code><br \/>\r\n<code> lambda_virus.3.bt2<\/code><br \/>\r\n<code> lambda_virus.4.bt2<\/code><br \/>\r\n<code> lambda_virus.rev.1.bt2<\/code><br \/>\r\n<code> lambda_virus.rev.2.bt2<\/code><br \/>\r\n<code> output.txt<\/code><br \/>\r\n<code> test_v2-2.2.9.sh<\/code><\/p>\r\n<ul>\r\n\t<li><strong>Others useful commands:<\/strong><\/li>\r\n<\/ul>\r\n<p><strong>On genologin servers<\/strong>, to find the path of\u00a0 the \"How_to_use_SLURM_soft_name\" file, use module help command:<\/p>\r\n<p><code>$ module help bioinfo\/bowtie2-2.2.9<\/code><\/p>\r\n<p><code>----------- Module Specific Help for 'bioinfo\/bowtie2-2.2.9' ---------------------------<\/code><\/p>\r\n<p><code>See How_to_use file: \/usr\/local\/bioinfo\/src\/bowtie\/How_to_use_SLURM_bowtie<\/code><\/p>\r\n<p><strong>In your web browser<\/strong>, to retrieve all \"How_to_use_SLURM_soft_name\" files:<\/p>\r\n<p><a href=\"http:\/\/vm-genobiotoul.toulouse.inra.fr\/How_to_Softs\/\">http:\/\/vm-genobiotoul.toulouse.inra.fr\/How_to_Softs\/<\/a><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse6\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to use module command ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse6\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>The basic command to use is module:<\/p>\r\n<p><code>module<\/code> : (no arguments) print usage instructions<code><br \/>\r\nmodule avail<\/code> : list available software module<br \/>\r\n <code>module load  <em>modulename<\/em><\/code> : add a module to your environment<br \/>\r\n <code>module unload <em>modulename<\/em><\/code> : unload remove a module<br \/>\r\n <code>module purge <\/code> : remove all modules<br \/>\r\n <code>module show <em>modulename<\/em><\/code> : show what changes a module will make to your environment<br \/>\r\n <code>module help <em>modulename<\/em><\/code> : path to the \"How_to_use_SLURM_soft_name\" file<\/p>\r\n<p>For more documentation, you can see the <a href=\"http:\/\/modules.sourceforge.net\/\" target=\"_blank\" rel=\"noopener\">Environment Module website<\/a>.<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse7\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to use R on the cluster SLURM?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse7\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Tutorial describing how to run R scripts and compile Rmarkdown files on genologin\/SLURM cluster:<\/p>\r\n<ul>\r\n\t<li><a href=\"http:\/\/www.nathalievialaneix.eu\/doc\/pdf\/tutoR_cluster.pdf\" target=\"_blank\">Tuto R<\/a><\/li>\r\n<\/ul>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse8\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to find an already install R package?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse8\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>On genologin.toulouse.inra.fr server with alias command \"search_R_package\" (case sensitive):<\/p>\r\n<p><code>search_R_package <em>package_name<\/em><\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse9\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to find if a Python package is already installed?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse9\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>On genologin.toulouse.inra.fr server with alias command \"search_Python_package\" (case insentitive):<\/p>\r\n<p><code>search_Python_package <em>package_name<\/em><\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse10\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tJava\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse10\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Launch java onto the nodes for the java command:<br \/>\r\n<code>java -Xmx4g<\/code><\/p>\r\n<p>Choose a specific java version:<br \/>\r\n<code>module load system\/Java8<\/code> (for java 8)<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse11\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tAvailable compilers\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse11\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>To <strong>see<\/strong> available compiler:<\/p>\r\n<p><code>module avail compiler<\/code><\/p>\r\n<p>Exemple to <strong>load<\/strong> a compiler:<\/p>\r\n<p><code>module load compiler\/gcc-7.2.0<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse12\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tCreate your own module\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse12\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<ul>\r\n\t<li><strong>Create modulefile with header:<\/strong><\/li>\r\n<\/ul>\r\n<p>#%Module1.0###############################################################<br \/>\r\n ##<\/p>\r\n<ul>\r\n\t<li><strong>Add environment:<\/strong><\/li>\r\n<\/ul>\r\n<p>module load existant module<br \/>\r\n prepend-path PATH \/usr\/local\/bioinfo\/src\/MultAlin\/multalin.5.4.1\/<br \/>\r\n setenv MULTALIN \/usr\/local\/bioinfo\/src\/MultAlin\/multalin.5.4.1\/<\/p>\r\n<ul>\r\n\t<li><strong>Load your module file:<\/strong><\/li>\r\n<\/ul>\r\n<p>module load -f \/path\/to\/your\/modulefile<\/p>\r\n<p><strong>Example:<\/strong><\/p>\r\n<ul>\r\n\t<li>Create your module:<\/li>\r\n<\/ul>\r\n<p><code>vi ~\/save\/my_own_module<\/code><\/p>\r\n<p>#%Module1.0###############################################################<br \/>\r\n ##<\/p>\r\n<p>module load bioinfo\/bowtie2-2.2.9<br \/>\r\n module load bioinfo\/bwa-0.7.15<br \/>\r\n module load bioinfo\/samtools-1.4<\/p>\r\n<p>prepend-path PATH \/usr\/local\/bioinfo\/src\/MultAlin\/multalin.5.4.1\/<br \/>\r\n setenv MULTALIN \/usr\/local\/bioinfo\/src\/MultAlin\/multalin.5.4.1\/<\/p>\r\n<ul>\r\n\t<li>Load your module:<\/li>\r\n<\/ul>\r\n<p><code>module load -f ~\/save\/my_own_module<\/code><\/p>\r\n<ul>\r\n\t<li>Environment verification:<\/li>\r\n<\/ul>\r\n<p><code>$ which bowtie2<\/code><br \/>\r\n \/usr\/local\/bioinfo\/src\/bowtie\/bowtie2-2.2.9\/bowtie2<\/p>\r\n<p><code>$ which bwa<\/code><br \/>\r\n \/usr\/local\/bioinfo\/src\/bwa\/bwa-0.7.15\/bwa<\/p>\r\n<p><code>$ which samtools<\/code><br \/>\r\n \/usr\/local\/bioinfo\/src\/samtools\/samtools-1.4\/samtools<\/p>\r\n<ul>\r\n\t<li>To unload one module:<\/li>\r\n<\/ul>\r\n<p><code>module unload bioinfo\/bowtie2-2.2.9<\/code><\/p>\r\n<ul>\r\n\t<li>To unload all module and specific variable:<\/li>\r\n<\/ul>\r\n<p><code>module purge<\/code><\/p>\r\n<p>\u00a0<\/p>\r\n<p>For more documentation, you can see the <a href=\"http:\/\/modules.sourceforge.net\/\" target=\"_blank\" rel=\"noopener\">Environment Module website<\/a>.<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2590 \" href=\"#ac_2590_collapse13\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tDefault directory for some software and \/home overquota\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2590_collapse13\" class=\"wpsm_panel-collapse collapse_2590 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Some software default directory (ex: .nextflow, .conda, .beast, .ncbi, .R ...) are usually located at your home directory whose allocated space is very limited.<br \/>\r\nA simple solution consist in create (or move if it already exist) .&lt;software&gt; directory in your work space and making a symbolic link to this<br \/>\r\ndirectory in your home<\/p>\r\n<p>Example with nextflow:<\/p>\r\n<p><code>mkdir ~\/work\/.nextflow<\/code> (or <code>mv ~\/.nextflow ~\/work\/<\/code>)<br \/>\r\n<code>ln -s ~\/work\/.nextflow\u00a0 ~\/.nextflow<\/code><\/p>\r\n<p>Example with conda:<\/p>\r\n<p><code>mkdir ~\/work\/.conda<\/code> (or <code>mv ~\/.conda ~\/work\/<\/code>)<br \/>\r\n<code>ln -s ~\/work\/.conda\u00a0\u00a0 ~\/.conda<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t<\/div>\r\n\t\t\t\t<script>\r\n\tjQuery(document).ready(function() {\r\n\t\t\r\n\t\t\tjQuery('.collapse_2590').on('shown.bs.collapse', function(){jQuery(this).parent().find(\".fa-plus\").removeClass(\"fa-minus\").addClass(\"fa-minus\"); jQuery(this).parent().find(\".wpsm_panel-heading\").addClass(\"acc-a\"); 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