## Argos/flybase-ng packages list #------- Common server packages ------------ package: argos-install package-alias: biodb-install description: Argos installation package url: rsync://iubio.bio.indiana.edu/argos/install/ url-fbdead: rsync://flybase.net/argos/install/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/install/ localpath: install/ updateexclude: run-apache run-postgres run-tomcat tomcatenv.sh package: argos-systems requires: argos-install description: Argos system-specific packages url: rsync://iubio.bio.indiana.edu/argos/common/systems/ url-fbdead: rsync://flybase.net/argos/common/systems/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/common/systems/ localpath: common/systems/ package: argos-common parts: logs common common/systems requires: argos-install description: Argos common server packages url: rsync://iubio.bio.indiana.edu/argos/ url-fbdead: rsync://flybase.net/argos/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/ localpath: updateexclude: servers/apache/conf/httpd.conf \ servers/tomcat/conf/server.xml \ servers/tomcat/webapps/*.xml # updateexc has to use localpath/parts path package: argos-root package-alias: biodb-root parts: ROOT docs description: Argos root server package url: rsync://iubio.bio.indiana.edu/argos/ url-fbdead: rsync://flybase.net/argos/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/ requires: argos-common localpath: updateexclude: conf/apache.conf conf/flybase*.conf is-main: true is-required: true est-size: 50 Mb package: argos-sources description: Argos common package sources url: rsync://iubio.bio.indiana.edu/argos/common/source/ url-fbdead: rsync://flybase.net/argos/common/source/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/common/source/ localpath: common/source/ is-main: true est-size: 100 Kb ## exclude-from: file ## exclude: patt-list ## updateexclude: -- files edited in reconfigure.conf ## add more exclude choices? developer parts like ant ; esp. dev-docs ? ## add 'template' ? ## add ftp/http fetch of rsync? but rsync.samba.org has binaries #------- FlyBase server ------------ package: flybase description: FlyBase Next Generation server package url: rsync://microbe.bio.indiana.edu/argos/flybase/ url-fbdead: rsync://flybase.net/argos/flybase/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/flybase/ alt-url: ftp://flybase.net/argos/flybase/ requires: argos-common flybase-data flybase-indices flybase-genomes flybase-blast bionet-drosophila exclude: indices localpath: flybase/ updateexclude: conf/apache.conf cgi-bin/fblocalenv.pl is-main: true est-size: 4 GB package: flybase-data description: FlyBase public data files url: rsync://microbe.bio.indiana.edu/argos/flybase/data/ url-fbdead: rsync://flybase.net/flybaseftp/flybase/ alt-url: ftp://flybase.net/flybase/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/flybase/data/ exclude: seqs/ maps/gnomap/ localpath: flybase/data/ ## retire seqs/ maps/gnomap/ from here, see below fban package: flybase-indices description: FlyBase data indices, database files url: rsync://microbe.bio.indiana.edu/argos/flybase/indices/ url-fbdead: rsync://flybase.net/argos/flybase/indices/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/flybase/indices/ alt-url: ftp://flybase.net/argos/flybase/indices/ localpath: flybase/indices/ old-url: rsync://flybase.net/fbserver/indices/ note-ftp: package flybase will get flybase/indices unless ftp exludes it # localpath: flybase/indices/ ## this now included w/ flybase-genomes ## ? revise this to set up symlinks to genomes/blast/ and miscellany/blast ? ## ? use above flybase-indices/blast to hande ? package: flybase-blast-OLD description: FlyBase BLAST indices url: rsync://flybase.net/flybaseftp/genomes/Drosophila_melanogaster/blastdb/ alt-url: ftp://flybase.net/genomes/Drosophila_melanogaster/blastdb/ localpath: flybase/indices/blast/ is-obsolete: true package: bionet-drosophila description: bionet drosophila news archive url: rsync://iubio.bio.indiana.edu/iubio/usenet/bionet/drosophila/ url-fbdead: rsync://flybase.net/flybaseftp/usenet/bionet/drosophila/ alt-url: ftp://flybase.net/usenet/bionet/drosophila/ url-uk: rsync://fbserver.gen.cam.ac.uk/argos/flybase/usenet/bionet/drosophila/ localpath: flybase/usenet/bionet/drosophila/ # ? revise this to set up symlinks to genomes/blast/ and miscellany/blast ? package: flybase-blast description: FlyBase BLAST indices #url: rsync://flybase.net/flybaseftp/genomes/Drosophila_melanogaster/blast_misc/ requires: flybase-dmel-blast_misc flybase-dpse-blast_misc localpath: flybase/indices/blastsets/ #? delete-folder: flybase/indices/blast/ package: flybase-dmel-blast_misc description: FlyBase BLAST indices dmel url: rsync://flybase.net/flybaseftp/genomes/Drosophila_melanogaster/blast_misc/ alt-url: ftp://flybase.net/genomes/Drosophila_melanogaster/blast_misc/ localpath: flybase/indices/blastsets/dmel_misc/ package: flybase-dpse-blast_misc description: FlyBase BLAST indices dpse url: rsync://flybase.net/flybaseftp/genomes/Drosophila_pseudoobscura/blast_misc/ alt-url: ftp://flybase.net/genomes/Drosophila_pseudoobscura/blast_misc/ localpath: flybase/indices/blastsets/dpse_misc/ ## aug04; change flybase-blast to flybase-genomes? with exclude choices for species... ## need to pre-mkdir flybase/data/genomes/$Species for this to work ! package: flybase-genomes description: FlyBase Genomes data, including Dmel and other Drosophila #url: rsync://flybase.net/flybaseftp/genomes/ #alt-url: ftp://flybase.net/genomes/ localpath: flybase/data/genomes/ requires: flybase-dmel-genome flybase-dmel-hetchr flybase-dpse-genome exclude: fasta/ fff/ gff/ pgsql/ xml-chado/ xml-game/ centaur/ # keep: blast/ dna/ gnomap/ fbobs/ srs/ &/or indices/ # want to rearrange storage/replicating fbobs/acode & indices/ - keep per release folder # but copy into flybase/indices/xxx and flybase/data(2)/fbobs w/o symlinks ? # parts: Drosophila_melanogaster/current/ Drosophila_melanogaster/current_hetchr/ # Drosophila_pseudoobscura/current/ # include fasta/*-all-* BUT need uncompressed at target; how to rsync .gz to non-gz ? package: flybase-dmel-genome description: FlyBase D. melanogaster genome data (euchromatin) url: rsync://flybase.net/flybaseftp/genomes/Drosophila_melanogaster/current/ alt-url: ftp://flybase.net/genomes/Drosophila_melanogaster/current/ localpath: flybase/data/genomes/Drosophila_melanogaster/current/ exclude: fasta/ fff/ gff/ pgsql/ xml-chado/ xml-game/ est-size: 4 GB package: flybase-dmel-hetchr description: DHGP/FlyBase D. melanogaster genome data (heterochromatin) url: rsync://flybase.net/flybaseftp/genomes/Drosophila_melanogaster/current_hetchr/ alt-url: ftp://flybase.net/genomes/Drosophila_melanogaster/current_hetchr/ localpath: flybase/data/genomes/Drosophila_melanogaster/current_hetchr/ exclude: fasta/ fff/ gff/ pgsql/ xml-chado/ xml-game/ est-size: 110 Mb package: flybase-dpse-genome description: FlyBase D. pseudoobscura genome data url: rsync://flybase.net/flybaseftp/genomes/Drosophila_pseudoobscura/current/ alt-url: ftp://flybase.net/genomes/Drosophila_pseudoobscura/current/ localpath: flybase/data/genomes/Drosophila_pseudoobscura/current/ exclude: fasta/ fff/ gff/ pgsql/ xml-chado/ xml-game/ est-size: 1.5 GB ## genomes/ is moving target - want mostly just current/ but options for ## other species and for dmel/current_hetero; add each as package? # package: flybase-annot-r320 # description: FlyBase Release r3.2.0_03162004 annotation data # url: rsync://flybase.net/flybaseftp/genomes/Drosophila_melanogaster/dmel_r3.2.0_03162004/ # alt-url: ftp://flybase.net/genomes/Drosophila_melanogaster/dmel_r3.2.0_03162004/ # localpath: flybase/data2/fban/r3.2.0_03162004/ # # exclude: *.gz xml-game/ xml-chado/ pgsql/ gff/ feats-all/ #^^ this should be optional include/exclude ... #include: blast fasta fbobs gnomap srs ##? break this down to sub-packages for localpath: ? ## need also symlink patches ... as postinstall doShell() for installargos.pl? # package: flybase-prerelease-fban320 # description: FlyBase Pre-release r3.2.0_12052003 data # url: rsync://flybase.net/argos/flybase-prerelease/fban/r3.2.0_12052003/ # localpath: flybase/data2/fban/r3.2.0_12052003/ ## need also symlink patches ... as postinstall doShell() for installargos.pl? #?? can do as simple package - make separate parts ?? # package: flybase-prerelease # description: FlyBase Pre-release data # url: rsync://flybase.net/argos/flybase-prerelease/ # localpath: flybase/prerelease/ # package: flybase-prerelease-fban310 # description: FlyBase Pre-release r3.1.0_12182003 data # url: rsync://flybase.net/argos/flybase-prerelease/fban/r3.1.0_12182003/ # localpath: flybase/data2/fban/r3.1.0_12182003/ # package: flybase-etc-old # description: FlyBase miscellany data, configs, etc. # url: rsync://flybase.net/argos/flybase/etc/ # localpath: flybase/etc/ # old-url: rsync://flybase.net/fbserver/server/.etc/ # old-exclude: gnomap/ tomcat/ grmap/pix/ perlbio/ expdb/ gmod-fb/ jdata/ jdata3/ jlib/ mysql/ plib/ prefs/ tomcat/ japp/armview/ japp/ribbon/ # note: updates to flybase-ng in progress for this section; source out-of-date \n # nov03 - copied old-public etc into flybase-ng/argos; this package is obsolete #------- euGenes server ------------ # changed from 'biodb' to 'argos' main public name; 17jun03 package: eugenes description: euGenes server package url: rsync://eugenes.org/argos/eugenes/ requires: argos-common localpath: eugenes/ # temp exclude big, unneeded data temps exclude: blastout.* hgtable.all updateexclude: conf/apache.conf note3: nov03 - all of eugenes data, indices now included in this reference argos is-main: true est-size: 10 GB #------- sample CentaurBase server ------------ #? home in flybase.net or eugenes.org package: centaurbase description: CentaurBase sample (mythical) service for Argos url: rsync://flybase.net/argos/centaurbase/ requires: argos-common argos-root centaurbase-data localpath: centaurbase/ updateexclude: conf/apache.conf is-main: true est-size: 50 Mb package: centaurbase-data description: CentaurBase sample (mythical) data for Argos url: rsync://flybase.net/flybaseftp/genomes/centaur/ localpath: centaurbase/data/ #------- sample GMOD database install ------------ package: gmod description: sample GMOD database install url: rsync://eugenes.org/argos/gmod/ requires: argos-common argos-root localpath: gmod/ updateexclude: conf/apache.conf is-main: true est-size: 50 Mb # add gmod-data: GO, SO ontologies? other genome data? #------- Daphnia wFleabase server ------------ # not yet publicly available package: daphnia description: Daphnia wFleabase - not yet publicly available note: not yet publicly available is-main: true est-size: 0 # url: # localpath: daphnia/ # updateexclude: conf/apache.conf # est-size: 50 Mb # package: daphnia-data # description: Daphnia wFleabase data # url: # localpath: