1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/2b27b1e42fc9/
changeset: 2b27b1e42fc9
user: dan
date: 2012-03-24 01:50:32
summary: Remove print debug.
affected #: 1 file
diff -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 -r 2b27b1e42fc90c4077c9ddcb963612efab28d940 lib/galaxy/openid/providers.py
--- a/lib/galaxy/openid/providers.py
+++ b/lib/galaxy/openid/providers.py
@@ -76,7 +76,6 @@
for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems():
if store_pref_value_name in ( self.sreg_optional + self.sreg_required ):
trans.user.preferences[ store_pref_name ] = sreg_attributes.get( store_pref_value_name )
- print 'setting',store_pref_name,'to',trans.user.preferences[ store_pref_name ]
else:
raise Exception( 'Only sreg is currently supported.' )
trans.sa_session.add( trans.user )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/463fc935b97c/
changeset: 463fc935b97c
user: dannon
date: 2012-03-23 13:59:34
summary: Convert loc file examples to use tabs instead of spaces.
affected #: 22 files
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample
+++ b/tool-data/all_fasta.loc.sample
@@ -4,13 +4,13 @@
#all_fasta.loc. This file has the format (white space characters are
#TAB characters):
#
-#<unique_build_id><dbkey><display_name><file_path>
+#<unique_build_id><dbkey><display_name><file_path>
#
#So, all_fasta.loc could look something like this:
#
-#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
-#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
-#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
#
#Your all_fasta.loc file should contain an entry for each individual
#fasta file. So there will be multiple fasta files for each build,
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb.loc.sample
--- a/tool-data/blastdb.loc.sample
+++ b/tool-data/blastdb.loc.sample
@@ -2,7 +2,7 @@
#list of nucleotide BLAST databases, using three columns tab separated
#(longer whitespace are TAB characters):
#
-#<unique_id><database_caption><base_name_path>
+#<unique_id><database_caption><base_name_path>
#
#The captions typically contain spaces and might end with the build date.
#It is important that the actual database name does not have a space in it,
@@ -25,9 +25,9 @@
#Your blastdb.loc file should include an entry per line for each "base name"
#you have stored. For example:
#
-#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
-#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk
-#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test
+#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk
+#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk
+#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test
#...etc...
#
#See also blastdb_p.loc which is for any protein BLAST database.
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb_p.loc.sample
--- a/tool-data/blastdb_p.loc.sample
+++ b/tool-data/blastdb_p.loc.sample
@@ -2,25 +2,25 @@
#list of protein BLAST databases, using three columns tab separated
#(longer whitespace are TAB characters):
#
-#<unique_id><database_caption><base_name_path>
+#<unique_id><database_caption><base_name_path>
#
#The captions typically contain spaces and might end with the build date.
#It is important that the actual database name does not have a space in it,
#and that the first tab that appears in the line is right before the path.
#
-#So, for example, if your database is NR and the path to your base name
+#So, for example, if your database is NR and the path to your base name
#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this:
#
-#nr NCBI NR (non redundant) /data/blastdb/nr
+#nr NCBI NR (non redundant) /data/blastdb/nr
#
#and your /data/blastdb directory would contain all of the files associated
#with the database, /data/blastdb/nr.*.
#
-#Your blastdb_p.loc file should include an entry per line for each "base name"
+#Your blastdb_p.loc file should include an entry per line for each "base name"
#you have stored. For example:
#
-#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr
-#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr
+#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr
+#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr
#...etc...
#
#See also blastdb.loc which is for any nucleotide BLAST database.
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bowtie_indices_color.loc.sample
--- a/tool-data/bowtie_indices_color.loc.sample
+++ b/tool-data/bowtie_indices_color.loc.sample
@@ -5,7 +5,7 @@
#the directories in which those files are stored. The bowtie_indices.loc
#file has this format (longer white space characters are TAB characters):
#
-#<unique_build_id><dbkey><display_name><file_base_path>
+#<unique_build_id><dbkey><display_name><file_base_path>
#
#So, for example, if you had hg18 indexed stored in
#/depot/data2/galaxy/bowtie/hg18/,
@@ -25,9 +25,9 @@
#index set you have stored. The "file" in the path does not actually
#exist, but it is the prefix for the actual index files. For example:
#
-#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
-#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
-#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
#...etc...
#
#Note that for backwards compatibility with workflows, the unique ID of
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index.loc.sample
--- a/tool-data/bwa_index.loc.sample
+++ b/tool-data/bwa_index.loc.sample
@@ -25,10 +25,10 @@
#index set you have stored. The "file" in the path does not actually
#exist, but it is the prefix for the actual index files. For example:
#
-#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
-#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
-#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
-#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
#...etc...
#
#Note that for backwards compatibility with workflows, the unique ID of
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index_color.loc.sample
--- a/tool-data/bwa_index_color.loc.sample
+++ b/tool-data/bwa_index_color.loc.sample
@@ -5,7 +5,7 @@
#the directories in which those files are stored. The bwa_index_color.loc
#file has this format (longer white space characters are TAB characters):
#
-#<unique_build_id><dbkey><display_name><file_path>
+#<unique_build_id><dbkey><display_name><file_path>
#
#So, for example, if you had phiX indexed stored in
#/depot/data2/galaxy/phiX/color/,
@@ -25,10 +25,10 @@
#index set you have stored. The "file" in the path does not actually
#exist, but it is the prefix for the actual index files. For example:
#
-#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa
-#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa
-#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa
-#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa
#...etc...
#
#Note that for backwards compatibility with workflows, the unique ID of
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/faseq.loc.sample
--- a/tool-data/faseq.loc.sample
+++ b/tool-data/faseq.loc.sample
@@ -20,7 +20,7 @@
#Your faseq.loc file should include an entry per line for each set of fasta
#sequence files you have stored. For example:
#
-#hg18 /depot/data2/galaxy/faseq/hg18
-#mm9 /depot/data2/galaxy/faseq/mm9
-#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis
+#hg18 /depot/data2/galaxy/faseq/hg18
+#mm9 /depot/data2/galaxy/faseq/mm9
+#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis
#...etc...
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gatk_sorted_picard_index.loc.sample
--- a/tool-data/gatk_sorted_picard_index.loc.sample
+++ b/tool-data/gatk_sorted_picard_index.loc.sample
@@ -5,13 +5,13 @@
#the directories in which those files are stored. The picard_index.loc
#file has this format (longer white space is the TAB character):
#
-#<unique_build_id><dbkey><display_name><fasta_file_path>
+#<unique_build_id><dbkey><display_name><fasta_file_path>
#
#So, for example, if you had hg18 indexed and stored in
-#/depot/data2/galaxy/srma/hg18/,
+#/depot/data2/galaxy/srma/hg18/,
#then the srma_index.loc entry would look like this:
#
-#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
#
#and your /depot/data2/galaxy/srma/hg18/ directory
#would contain the following three files:
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.chrlens.loc.sample
--- a/tool-data/gd.chrlens.loc.sample
+++ b/tool-data/gd.chrlens.loc.sample
@@ -6,17 +6,17 @@
# file has the following format (white space characters are TAB
# characters):
#
-#<species><reference_species_file_path>
+#<species><reference_species_file_path>
#
# So, for example, if you used Monodelphis domestica as the reference
# species for a collection of Sarcophilus harrisii SNPs, then the
# gd.chrlens.loc entry would look like this:
#
-#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt
+#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt
#
# Your gd.chrlens.loc file should include an entry for each pair of
# species SNPs and reference species. For example:
#
-#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt
-#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt
+#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt
+#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt
#...etc...
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.primers.loc.sample
--- a/tool-data/gd.primers.loc.sample
+++ b/tool-data/gd.primers.loc.sample
@@ -5,18 +5,18 @@
# primers files are stored. The gd.primers.loc file has the following
# format (white space characters are TAB characters):
#
-#<species><primers_file_path>
+#<species><primers_file_path>
#
# So, for example, if you had a primers file located at
# /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of
# Ovis canadensis SNPs, then the gd.primers.loc entry would look like
# this:
#
-#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt
+#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt
#
# Your gd.primers.loc file should include an entry for each pair of
# species SNPs and primers file. For example:
#
-#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt
-#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt
+#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt
+#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt
#...etc...
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.snps.loc.sample
--- a/tool-data/gd.snps.loc.sample
+++ b/tool-data/gd.snps.loc.sample
@@ -5,17 +5,17 @@
# SNP call files are stored. The gd.snps.loc file has the following
# format (white space characters are TAB characters):
#
-#<species><SNP_call_file_path>
+#<species><SNP_call_file_path>
#
# So, for example, if you had a SNP call file located at
# /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of
# Ovis canadensis SNPs, then the gd.snps.loc entry would look like this:
#
-#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt
+#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt
#
# Your gd.snps.loc file should include an entry for each pair of species
# SNPs and SNP call file. For example:
#
-#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt
-#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt
+#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt
+#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt
#...etc...
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/lastz_seqs.loc.sample
--- a/tool-data/lastz_seqs.loc.sample
+++ b/tool-data/lastz_seqs.loc.sample
@@ -5,13 +5,13 @@
#the directories in which those files are stored. The lastz_seqs.loc
#file has this format (white space characters are TAB characters):
#
-#<unique_build_id><display_name><file_path>
+#<unique_build_id><display_name><file_path>
#
#So, for example, if your lastz_seqs.loc began like this:
#
-#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
-#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
-#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
+#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
+#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
+#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
#
#then your /depot/data2/galaxy/twobit/ directory
#would need to contain the following 2bit files:
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/liftOver.loc.sample
--- a/tool-data/liftOver.loc.sample
+++ b/tool-data/liftOver.loc.sample
@@ -8,7 +8,7 @@
#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain,
#then the liftOver.loc entry would look like this:
#
-#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
#
#and your /depot/data2/galaxy/anoCar1/liftOver directory would
#contain all of your "chain" files (e.g.):
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/mosaik_index.loc.sample
--- a/tool-data/mosaik_index.loc.sample
+++ b/tool-data/mosaik_index.loc.sample
@@ -5,13 +5,13 @@
#the directories in which those files are stored. The mosaik_index.loc
#file has this format (longer white space is the TAB character):
#
-#<unique_build_id><dbkey><display_name><fasta_file_path>
+#<unique_build_id><dbkey><display_name><fasta_file_path>
#
#So, for example, if you had hg18 indexed and stored in
#/depot/data2/galaxy/mosaik/hg18/
#then the mosaik_index.loc entry would look like this:
#
-#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa
#
#and your /depot/data2/galaxy/mosaik/hg18/ directory
#would contain the following files:
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/ngs_sim_fasta.loc.sample
--- a/tool-data/ngs_sim_fasta.loc.sample
+++ b/tool-data/ngs_sim_fasta.loc.sample
@@ -4,17 +4,17 @@
#in this directory) that points to the locations of those files. The ngs_sim.loc
#file has this format (white space characters are TAB characters):
#
-#<unique_build_id><dbkey><display_name><file_base_path>
+#<unique_build_id><dbkey><display_name><file_base_path>
#
#So, for example, if you had hg18chrM.fa in
#/data/path/hg18/seq/,
#then the ngs_sim.loc entry would look like this:
#
-#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa
+#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa
#
#Your ngs_sim.loc file should include an entry per line for each FASTA file you
#have stored.
#
-#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa
-#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa
-#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa
+#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa
+#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa
+#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_base_index.loc.sample
--- a/tool-data/perm_base_index.loc.sample
+++ b/tool-data/perm_base_index.loc.sample
@@ -5,7 +5,7 @@
#the directories in which those files are stored. The perm_base_index.loc
#file has this format (longer white space characters are TAB characters):
#
-#<build_seed_readlength><display_name><file_base>
+#<build_seed_readlength><display_name><file_base>
#
#Because each PerM index is built with a specific seed and a specific read
#length, this needs to be specified so the user can choose the appropriate
@@ -13,7 +13,7 @@
#50, and stored in /depot/data/galaxy/phiX/perm_index/,
#then the perm_base_index.loc entry would look something like this:
#
-#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
#
#and your /depot/data/galaxy/phiX/perm_index/ directory
#would contain the file phiX_base_F3_50.index:
@@ -21,7 +21,7 @@
#Your perm_base_index.loc file should include an entry per line for each
#index set you have stored. For example:
#
-#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
-#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
-#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
-#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
+#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
+#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_color_index.loc.sample
--- a/tool-data/perm_color_index.loc.sample
+++ b/tool-data/perm_color_index.loc.sample
@@ -5,7 +5,7 @@
#the directories in which those files are stored. The perm_color_index.loc
#file has this format (white space characters are TAB characters):
#
-#<build_seed_readlength><display_name><file_base>
+#<build_seed_readlength><display_name><file_base>
#
#Because each PerM index is built with a specific seed and a specific read
#length, this needs to be specified so the user can choose the appropriate
@@ -13,7 +13,7 @@
#50, and stored in /depot/data/galaxy/phiX/perm_index/,
#then the perm_color_index.loc entry would look something like this:
#
-#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
#
#and your /depot/data/galaxy/phiX/perm_index/ directory
#would contain the file phiX_color_F3_50.index:
@@ -21,8 +21,8 @@
#Your perm_color_index.loc file should include an entry per line for each
#index set you have stored. For example:
#
-#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
-#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
-#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
-#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
+#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
+#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
#
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/picard_index.loc.sample
--- a/tool-data/picard_index.loc.sample
+++ b/tool-data/picard_index.loc.sample
@@ -5,13 +5,13 @@
#the directories in which those files are stored. The picard_index.loc
#file has this format (longer white space is the TAB character):
#
-#<unique_build_id><dbkey><display_name><fasta_file_path>
+#<unique_build_id><dbkey><display_name><fasta_file_path>
#
#So, for example, if you had hg18 indexed and stored in
#/depot/data2/galaxy/srma/hg18/,
#then the srma_index.loc entry would look like this:
#
-#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
#
#and your /depot/data2/galaxy/srma/hg18/ directory
#would contain the following three files:
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/quality_scores.loc.sample
--- a/tool-data/quality_scores.loc.sample
+++ b/tool-data/quality_scores.loc.sample
@@ -8,7 +8,7 @@
#/depot/data2/galaxy/panTro2/quality_scores, then the quality_scores.loc entry
#would look like this:
#
-#panTro2 /depot/data2/galaxy/panTro2/quality_scores
+#panTro2 /depot/data2/galaxy/panTro2/quality_scores
#
#and your /depot/data2/galaxy/panTro2/quality_scores directory would
#contain all of your quality score files (e.g.):
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/regions.loc.sample
--- a/tool-data/regions.loc.sample
+++ b/tool-data/regions.loc.sample
@@ -8,7 +8,7 @@
#/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the
#regions.loc entry would look like this:
#
-#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed
+#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed
#
#and your /depot/data2/galaxy/regions/ directory would
#contain all of your regions files (e.g.):
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/srma_index.loc.sample
--- a/tool-data/srma_index.loc.sample
+++ b/tool-data/srma_index.loc.sample
@@ -8,13 +8,13 @@
#the directories in which those files are stored. The srma_index.loc
#file has this format (longer white space is the TAB character):
#
-#<unique_build_id><dbkey><display_name><fasta_file_path>
+#<unique_build_id><dbkey><display_name><fasta_file_path>
#
#So, for example, if you had hg18 indexed and stored in
#/depot/data2/galaxy/srma/hg18/,
#then the srma_index.loc entry would look like this:
#
-#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa
#
#and your /depot/data2/galaxy/srma/hg18/ directory
#would contain the following three files:
diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/twobit.loc.sample
--- a/tool-data/twobit.loc.sample
+++ b/tool-data/twobit.loc.sample
@@ -8,7 +8,7 @@
#/depot/data2/galaxy/droPer1/, then the twobit.loc entry
#would look like this:
#
-#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
+#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
#
#and your /depot/data2/galaxy/droPer1/ directory would
#contain all of your twobit files (e.g.):
@@ -19,8 +19,8 @@
#Your twobit.loc file should include an entry per line for each twobit
#file you have stored. For example:
#
-#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
-#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit
-#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit
-#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit
+#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit
#...etc...
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/732c10115fdf/
changeset: 732c10115fdf
user: dannon
date: 2012-03-23 13:24:42
summary: =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample
affected #: 1 file
diff -r 1adcc1b43718a0abc925061fdb6403a60bde2ddb -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e tool-data/bowtie_indices.loc.sample
--- a/tool-data/bowtie_indices.loc.sample
+++ b/tool-data/bowtie_indices.loc.sample
@@ -7,11 +7,11 @@
#
#<unique_build_id><dbkey><display_name><file_base_path>
#
-#So, for example, if you had hg18 indexed stored in
-#/depot/data2/galaxy/bowtie/hg18/,
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
#then the bowtie_indices.loc entry would look like this:
#
-#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
#
#and your /depot/data2/galaxy/bowtie/hg18/ directory
#would contain hg18.*.ebwt files:
@@ -25,9 +25,9 @@
#index set you have stored. The "file" in the path does not actually
#exist, but it is the prefix for the actual index files. For example:
#
-#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
-#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
-#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
#...etc...
#
#Note that for backwards compatibility with workflows, the unique ID of
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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changeset: b7d0ea8cf233
user: jgoecks
date: 2012-03-22 23:53:55
summary: Reinstate dialog-box class in modal.
affected #: 1 file
diff -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae -r b7d0ea8cf2334a840b9bef195c06b30e99fcbaba templates/base_panels.mako
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -178,7 +178,7 @@
<div id="overlay-background" class="modal-backdrop fade ${overlay_class}"></div>
- <div id="dialog-box" class="modal" border="0" ${display}>
+ <div id="dialog-box" class="modal dialog-box" border="0" ${display}><div class="modal-header"><span><h3 class='title'>${title}</h3></span></div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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changeset: 423d7f6e7b80
user: jgoecks
date: 2012-03-22 23:00:54
summary: Remove debugging statement.
affected #: 1 file
diff -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae static/scripts/galaxy.panels.js
--- a/static/scripts/galaxy.panels.js
+++ b/static/scripts/galaxy.panels.js
@@ -140,7 +140,6 @@
}
// Buttons
this.$footer.hide();
- console.log( this.$footer, options.buttons );
var $buttons = this.$footer.find( ".buttons" ).html( "" );
if ( options.buttons ) {
$.each( options.buttons, function( name, value ) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
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changeset: bb19e940a03c
user: richard_burhans
date: 2012-03-22 21:15:24
summary: fix get_file_peek() to better support datasets with very long lines
affected #: 1 file
diff -r fa40b8f3f385f67d57294d98a036e483775d873f -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -433,13 +433,13 @@
if line and not line.startswith( '#' ):
data_lines += 1
return data_lines
- def set_peek( self, dataset, line_count=None, is_multi_byte=False, skipchars=[] ):
+ def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=[] ):
"""
Set the peek. This method is used by various subclasses of Text.
"""
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
- dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, skipchars=skipchars )
+ dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars )
if line_count is None:
# See if line_count is stored in the metadata
if dataset.metadata.data_lines:
@@ -567,6 +567,11 @@
## >>> get_file_peek(fname)
## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n'
"""
+ # Set size for file.readline() to a negative number to force it to
+ # read until either a newline or EOF. Needed for datasets with very
+ # long lines.
+ if WIDTH == 'unlimited':
+ WIDTH = -1
lines = []
count = 0
file_type = None
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