MediaWiki API result

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    "continue": {
        "gapcontinue": "Reopening_of_Euler_and_Leonhard_(May_2020)",
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    "query": {
        "pages": {
            "639": {
                "pageid": 639,
                "ns": 0,
                "title": "Reference genomes",
                "revisions": [
                    {
                        "contentformat": "text/x-wiki",
                        "contentmodel": "wikitext",
                        "*": "==Illumina igenomes (Euler)==\n\nIn /cluster/project/igenomes, we provide a set of reference genomes and annotations (illumina igenomes) for a selection of model organism. The genomes and annotations were downloaded from\n\n https://support.illumina.com/sequencing/sequencing_software/igenome.html\n\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Arabidopsis_thaliana/Ensembl/TAIR10\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Arabidopsis_thaliana/NCBI/TAIR10\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Bacillus_cereus_ATCC_10987/NCBI/2004-02-13\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Bacillus_subtilis_168/Ensembl/EB2\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 29  2014 Caenorhabditis_elegans/Ensembl/WBcel235\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Caenorhabditis_elegans/NCBI/WS195\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Caenorhabditis_elegans/UCSC/ce10\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Dec  1  2014 Drosophila_melanogaster/Ensembl/BDGP5.25\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Jul 29  2015 Drosophila_melanogaster/Ensembl/BDGP6\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Drosophila_melanogaster/NCBI/build5.41\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Jul 30  2015 Drosophila_melanogaster/UCSC/dm6\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Enterobacteriophage_lambda/NCBI/1993-04-28\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Escherichia_coli_K_12_DH10B/Ensembl/EB1\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Escherichia_coli_K_12_DH10B/NCBI/2008-03-17\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Escherichia_coli_K_12_MG1655/NCBI/2001-10-15\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Homo_sapiens/Ensembl/GRCh37\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Aug 18  2015 Homo_sapiens/NCBI/GRCh38\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Dec  1  2014 Homo_sapiens/UCSC/hg19\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Aug 18  2015 Homo_sapiens/UCSC/hg38\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Dec  1  2014 Mus_musculus/Ensembl/NCBIM37\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Mus_musculus/NCBI/GRCm38\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Mus_musculus/UCSC/mm10\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Mycobacterium_tuberculosis_H37RV/NCBI/2001-09-07\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 PhiX/Illumina/RTA\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 PhiX/NCBI/1993-04-28\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Pseudomonas_aeruginosa_PAO1/NCBI/2000-09-13\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Jul 31  2015 Rattus_norvegicus/Ensembl/Rnor_6.0\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Jul 31  2015 Rattus_norvegicus/NCBI/Rnor_6.0\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 Jul 31  2015 Rattus_norvegicus/UCSC/rn6\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Rhodobacter_sphaeroides_2.4.1/NCBI/2005-10-07\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 29  2014 Saccharomyces_cerevisiae/Ensembl/R64-1-1\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Saccharomyces_cerevisiae/NCBI/build3.1\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Saccharomyces_cerevisiae/UCSC/sacCer3\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Schizosaccharomyces_pombe/Ensembl/EF2\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Sorangium_cellulosum_So_ce_56/NCBI/2007-11-27\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Sorghum_bicolor/Ensembl/Sbi1\n drwxr-xr-x 4 apps ID-HPC-APPS 4096 May 28  2014 Staphylococcus_aureus_NCTC_8325/NCBI/2006-02-13\n\n==Reference genomes (Leonhard Open)==\nIn /cluster/work/genomes users can find reference genomes for a selection or organisms.\n\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:14 Adapters\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:14 Arabidopsis\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:14 Caenorhabditis_elegans\n drwxr-s--- 7 sfux T0000 4096 Jul 21 08:17 CellRanger\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:19 Drosophila\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:19 E_coli\n drwxr-sr-x 4 sfux T0000 4096 Jul 21 08:22 Homo_sapiens\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:24 Lambda\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:24 Mus_musculus\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:24 Mitochondria\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:37 Rattus_norvegicus\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:37 PhiX\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:40 Saccharomyces_cerevisiae\n drwxr-sr-x 3 sfux T0000 4096 Jul 21 08:40 Vectors"
                    }
                ]
            },
            "1504": {
                "pageid": 1504,
                "ns": 0,
                "title": "Rendering without display",
                "revisions": [
                    {
                        "contentformat": "text/x-wiki",
                        "contentmodel": "wikitext",
                        "*": "==Introduction==\nRendering images on a remote HPC is slightly different from rendering images on your local computer, because the compute nodes in Euler don't have a display attached. The most suitable solution for  is, when the software itself provides offscreen rendering, but it can also be done using a virtual frame buffer.\n\n==Offscreen rendering with OSMesa or EGL==\nPlease find below some links that provide information about how to use OSMesa or EGL for offscreen rendering:\n\n https://docs.mesa3d.org/osmesa.html\n https://blog.kitware.com/off-screen-rendering-through-the-native-platform-interface-egl/\n\n==Virtual frame buffer==\nXvfb is a virtual framebuffer that is part of the X11 libraries. It is installed on Euler as a part of the operating system. By prefixing the command with <tt>xvfb-run -a</tt> the rendering is done in a frame buffer:\n \n sbatch [Slurm options] --wrap=\"xvfb-run -a my_command_that_does_the_rendering\"\n\nPlease find below the available options for xvfb-run:\n\n [sfux@eu-login-33 ~]$ xvfb-run --help\n Usage: xvfb-run [OPTION ...] COMMAND\n Run COMMAND (usually an X client) in a virtual X server environment.\n Options:\n -a        --auto-servernum          try to get a free server number, starting at\n                                     --server-num (deprecated, use --auto-display\n                                     instead)\n -d        --auto-display            use the X server to find a display number\n                                     automatically\n -e FILE   --error-file=FILE         file used to store xauth errors and Xvfb\n                                     output (default: /dev/null)\n -f FILE   --auth-file=FILE          file used to store auth cookie\n                                     (default: ./.Xauthority)\n -h        --help                    display this usage message and exit\n -n NUM    --server-num=NUM          server number to use (default: 99)\n -l        --listen-tcp              enable TCP port listening in the X server\n -p PROTO  --xauth-protocol=PROTO    X authority protocol name to use\n                                     (default: xauth command's default)\n -s ARGS   --server-args=ARGS        arguments (other than server number and\n                                     \"-nolisten tcp\") to pass to the Xvfb server\n                                     (default: \"-screen 0 640x480x8\")\n -w DELAY  --wait=DELAY              delay in seconds to wait for Xvfb to start\n                                     before running COMMAND (default: 3)\n [sfux@eu-login-33 ~]$"
                    }
                ]
            }
        }
    }
}