# HG changeset patch # User vimalkumarvelayudhan # Date 1519812051 18000 # Node ID ff53c4ab725790835943b9147c6240a8846b0631 # Parent 957d6a4f11269fc59523f46a29b0657abcbcd058 Uploaded diff -r 957d6a4f1126 -r ff53c4ab7257 tool-data/viga_blastdb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/viga_blastdb.loc.sample Wed Feb 28 05:00:51 2018 -0500 @@ -0,0 +1,31 @@ +# viga_blastdb.loc +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# +# +# So, for example, if you had hg18 indexes stored in: +# +# /data/databases/blast/nr/nr +# +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 +# +# then the viga_blastdb.loc entry could look like this: + +#nr nr Non_redundant (nr) /data/databases/blast/nr/nr +#swissprot swissprot Swissprot (swissprot) /data/databases/blast/swissprot/swissprot diff -r 957d6a4f1126 -r ff53c4ab7257 tool-data/viga_diamonddb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/viga_diamonddb.loc.sample Wed Feb 28 05:00:51 2018 -0500 @@ -0,0 +1,5 @@ +# +# + +#nr nr Non_redundant (nr) /data/databases/diamonddb/nr +#swissprot swissprot Swissprot (swissprot) /data/databases/diamonddb/swissprot diff -r 957d6a4f1126 -r ff53c4ab7257 tool-data/viga_hmmdb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/viga_hmmdb.loc.sample Wed Feb 28 05:00:51 2018 -0500 @@ -0,0 +1,5 @@ +# +# +#uniprot_trembl uniprot_trembl UniProt TrEMBL /data/databases/SwissProt_UniProt/uniprot_trembl.fasta +#uniprot_sprot uniprot_sprot UniProt Swiss-Prot /data/databases/SwissProt_UniProt/uniprot_sprot.fasta + diff -r 957d6a4f1126 -r ff53c4ab7257 tool-data/viga_rfamdb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/viga_rfamdb.loc.sample Wed Feb 28 05:00:51 2018 -0500 @@ -0,0 +1,4 @@ +# +# +#Rfam Rfam Rfam /data/databases/rfam/Rfam.cm + diff -r 957d6a4f1126 -r ff53c4ab7257 tool_data/viga_blastdb.loc.sample --- a/tool_data/viga_blastdb.loc.sample Tue Feb 27 14:43:59 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -# viga_blastdb.loc -# This is a *.loc.sample file distributed with Galaxy that enables tools -# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. -# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup -# First create these data files and save them in your own data directory structure. -# Then, create a bowtie_indices.loc file to use those indexes with tools. -# Copy this file, save it with the same name (minus the .sample), -# follow the format examples, and store the result in this directory. -# The file should include an one line entry for each index set. -# The path points to the "basename" for the set, not a specific file. -# It has four text columns seperated by TABS. -# -# -# -# So, for example, if you had hg18 indexes stored in: -# -# /data/databases/blast/nr/nr -# -# containing hg19 genome and hg19.*.bt2 files, such as: -# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa -# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 -# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 -# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 -# -# then the viga_blastdb.loc entry could look like this: - -#nr nr Non_redundant (nr) /data/databases/blast/nr/nr -#swissprot swissprot Swissprot (swissprot) /data/databases/blast/swissprot/swissprot diff -r 957d6a4f1126 -r ff53c4ab7257 tool_data/viga_diamonddb.loc.sample --- a/tool_data/viga_diamonddb.loc.sample Tue Feb 27 14:43:59 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -# -# - -#nr nr Non_redundant (nr) /data/databases/diamonddb/nr -#swissprot swissprot Swissprot (swissprot) /data/databases/diamonddb/swissprot diff -r 957d6a4f1126 -r ff53c4ab7257 tool_data/viga_hmmdb.loc.sample --- a/tool_data/viga_hmmdb.loc.sample Tue Feb 27 14:43:59 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -# -# -#uniprot_trembl uniprot_trembl UniProt TrEMBL /data/databases/SwissProt_UniProt/uniprot_trembl.fasta -#uniprot_sprot uniprot_sprot UniProt Swiss-Prot /data/databases/SwissProt_UniProt/uniprot_sprot.fasta - diff -r 957d6a4f1126 -r ff53c4ab7257 tool_data/viga_rfamdb.loc.sample --- a/tool_data/viga_rfamdb.loc.sample Tue Feb 27 14:43:59 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -# -# -#Rfam Rfam Rfam /data/databases/rfam/Rfam.cm -