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How to set up the blast server\n#==============================================\n\n# These instructions were tested for the versions below on \n# catskill.cshl.edu \n\n# CODE INSTALLATION\n#------------------\n\n# bash shell assumed\n# Set code/data versions (will change with each release)\n# These are just used for convenience for this README\nexport ENSVER=65\nexport GRAVER=34b\nexport EGVER=12\n\n# Fetch the version-specific code into a clean directory\nmkdir /usr/local/svntmp/ensembl-grmblast-$ENSVER\ncd /usr/local/svntmp/ensembl-grmblast-$ENSVER\n\ncvs -d :pserver:cvsuser@cvsro.sanger.ac.uk:/cvsroot/ensembl login\n[pass CVSUSER]\n\ncvs -d :pserver:cvsuser@cvsro.sanger.ac.uk:/cvsroot/ensembl \\\nco -r branch-ensembl-$ENSVER ensembl-api\n\ncvs -d :pserver:cvsuser@cvsro.sanger.ac.uk:/cvsroot/ensembl \\\nco -r branch-ensembl-$ENSVER ensembl-website\n\ncvs -d :pserver:cvsuser@cvsro.sanger.ac.uk:/cvsroot/ensembl \\\nco -r branch-ensemblgenomes-$EGVER-$ENSVER eg-plugins\n\nsvn co http://svn.warelab.org/gramene/branches/build${GRAVER}-branch \\\ngramene-$GRAVER\n\n# Move the code directory into place\nsudo mv /usr/local/svntmp/ensembl-grmblast-$ENSVER /usr/local\n\n# Create links to code that does not change\ncd /usr/local/ensembl-grmblast-$ENSVER \nln -s gramene-$GRAVER gramene-live\nln -s /usr/local/bioperl-1-2-3 bioperl-live\nln -s /usr/local/biomart-perl-0_6 biomart-perl\nln -s /usr/local/apache2 apache2\ncp /usr/local/vcftools_0.1.5/lib/Vcf.pm /usr/local/ensembl-grmblast/modules/\n\n# Create temporary dirs\nmkdir logs\nmkdir -p /usr/local/ensembl-grmblast/htdocs/BlastView/minified\n\n# Move the Ensembl Plugins file into place\ncp gramene-live/ensembl-plugins/grmblast/conf/Plugins.pm conf/\n\n# Stop the old server, and start the new\n# NOTE: the new server should have been tested first!\n\nsudo kill `cat /usr/local/ensembl-grmblast/logs/httpd.pid`\nsudo rm /usr/local/ensembl-grmblast\nsudo ln -s /usr/local/ensembl-grmblast-$ENSVER /usr/local/ensembl-grmblast\nsudo /etc/init.d/apachectl-grmblast start\n\n\n# DATA INSTALLATION\n#------------------\n\n# Get the version-specific FASTA databases\n# Note that we download these from the EnsemblGenomes FTP site, \n# But they can be generated direct from the Ensembl databases\n# using the utils/do_fasta_dump script\n\n##get sequences\n# for EG genomes, we can download from EG ftp site\n\nwget -nH -r --cut-dirs=3 \\\n\"ftp://ftp.ensemblgenomes.org/pub/release-$EGVER/plants/fasta/\"\n\n# for Gramene specific genomes such as OGE genomes, create locally\ncd ensembl-live/\nperl  utils/do_fasta_dump  \n\t--no_ssaha --species $s \n\t-type dna_toplevel -type cdna_all -type pep_all -type ncrna \n\t-dumpdir OGEdump/ \n\t-release 71 \n\t--no_log \n\t-email weix@cshl.edu;\n\n# Index the FASTA DBs\nfind fasta/ -name \\*.gz -exec gunzip {} \\;\nfind fasta/ -name \\*.pep.\\*.fa -exec /usr/local/wublast/xdformat -p {} \\;\nfind fasta/ -name \\*dna\\*.fa -exec /usr/local/wublast/xdformat -n {} \\;\n\n# Move the indexes into place, and update the symlink\nmkdir /usr/local/blastdb/gramene-$ENSVER\nfind fasta/ -name \\*.fa.x?? -exec mv {} /usr/local/blastdb/gramene-$ENSVER \\;\nsudo rm /usr/local/blastdb/gramene\nsudo ln -s /usr/local/blastdb/gramene-$ENSVER \\\n/usr/local/blastdb/gramene\n\n# Some slight renaming to convert from EG to Ensembl convention\ncd /usr/local/blastdb/gramene\nls | perl -e 'while(\u003c\u003e){ chomp; my $ori=$_; my $new=$ori; if( $ori =~ /^.*\\..*\\.(.*\\.).*\\..*\\.fa/..*$ ){ $new =~ s/$1//; `mv $ori $new` } }'\nFor example, the filename should be Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.* or Zea_mays.AGPv3.pep.all.fa.*\nThe format should be, and we only need *.dna.toplevel.fa.* and *.pep.all.fa.*, we do not need the individual chromosome files to be indexed,\nSpecies.assemblyVersion.dna.toplevel.fa.*\nSpecies.assemblyVersion.pep.all.fa.*\n\n# MAINTENANCE\n#------------\n\nEnsure that there is a startup script in /etc/init.d that is correctly\nlinked from /etc/rc.d to ensure that the web server is restarted on\nserver reboot.\n\nThere are also some scripts that need installing in the root user's\ncrontab that clean up temporary blast files and database records. Here\nis an example (please replace \u003cENSROOT\u003e with the value of the $ENSROOT\nvariable);\n\n---\n# Clean ensembl* tmp and img-tmp files, and the blast database\n0  4 * * * find \u003cENSROOT\u003e/*tmp -type f -atime +1 -exec rm {} \\; \u003e /dev/null 2\u003e\u00261\n0  4 * * * find \u003cENSROOT\u003e/img-cache -type f -atime +1 -exec rm {} \\; \u003e /dev/null 2\u003e\u00261\n0  3 * * * perl \u003cENSROOT\u003e/utils/blast_cleaner.pl \n---\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwarelab%2Fgramene-ensembl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwarelab%2Fgramene-ensembl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwarelab%2Fgramene-ensembl/lists"}