| Previous changeset 4:957d6a4f1126 (2018-02-27) |
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Commit message:
Uploaded |
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added:
tool-data/viga_blastdb.loc.sample tool-data/viga_diamonddb.loc.sample tool-data/viga_hmmdb.loc.sample tool-data/viga_rfamdb.loc.sample |
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removed:
tool_data/viga_blastdb.loc.sample tool_data/viga_diamonddb.loc.sample tool_data/viga_hmmdb.loc.sample tool_data/viga_rfamdb.loc.sample |
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| 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 |
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| @@ -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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# 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 |
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| 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 |
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| @@ -0,0 +1,5 @@ +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> + +#nr nr Non_redundant (nr) /data/databases/diamonddb/nr +#swissprot swissprot Swissprot (swissprot) /data/databases/diamonddb/swissprot |
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| 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 |
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| @@ -0,0 +1,5 @@ +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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 + |
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| 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 |
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| @@ -0,0 +1,4 @@ +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#Rfam Rfam Rfam /data/databases/rfam/Rfam.cm + |
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| 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 |
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| @@ -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. -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -# 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 |
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| 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 |
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| @@ -1,5 +0,0 @@ -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> - -#nr nr Non_redundant (nr) /data/databases/diamonddb/nr -#swissprot swissprot Swissprot (swissprot) /data/databases/diamonddb/swissprot |
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| 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 |
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| @@ -1,5 +0,0 @@ -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -#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 - |
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| 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 |
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| @@ -1,4 +0,0 @@ -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -#Rfam Rfam Rfam /data/databases/rfam/Rfam.cm - |