Daniel Blankenberg ab53cc6d3b First pass at adding Ensembl browsers as an external display application. Two different URL generation and data attachment methods are used; one for 'old' Ensembl archives older than ~November 2008 and another for Ensembl sites using the current method. The tool-data/shared/ensembl/ensembl_sites.txt file contains the site and build information for using the current method; the tool-data/shared/ensembl/ensembl_sites_data_URL.txt file has the site and build information for when the older method is to be used. ...

The new method follows: http://www.ensembl.org/info/docs/webcode/linking.html

The old method follows: http://aug2007.archive.ensembl.org/Homo_sapiens/helpview?se=1;kw=urlsource

2010-05-21 15:25:56 -04:00

..

shared

First pass at adding Ensembl browsers as an external display application. Two different URL generation and data attachment methods are used; one for 'old' Ensembl archives older than ~November 2008 and another for Ensembl sites using the current method. The tool-data/shared/ensembl/ensembl_sites.txt file contains the site and build information for using the current method; the tool-data/shared/ensembl/ensembl_sites_data_URL.txt file has the site and build information for when the older method is to be used.

2010-05-21 15:25:56 -04:00

add_scores.loc.sample

Add the add_scores tool.

2010-03-23 15:43:58 -04:00

alignseq.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00

annotation_profiler_options.xml.sample

SNP/WGA tool changes only

2010-05-10 10:17:11 -04:00

annotation_profiler_valid_builds.txt.sample

Adding a new parameter type drill_down. This parameter type creates a hierarchical set of checkboxes or radiobuttons.

2008-05-07 17:10:35 +00:00

binned_scores.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00

blastdb.loc.sample

Updated megablast_wrapper tool to allow for date to be included with database name and displayed (so user knows how current it is)

2009-12-09 18:50:12 -05:00

bowtie_indices_color.loc.sample

Added SOLiD (colorspace) support to Bowtie wrapper tool

2010-01-11 17:04:45 -05:00

bowtie_indices.loc.sample

Updated several sample index loc files to make it clearer how the actual loc files should appear

2009-10-07 15:31:18 -04:00

bwa_index.loc.sample

Removed SOLiD option from BWA, cleaned up Bowtie and BWA wrapper interfaces, and changed name of BWA index loc file

2010-01-22 10:49:38 -05:00

codingSnps.loc.sample

Add the codingSnps tool.

2010-03-23 13:53:21 -04:00

encode_datasets.loc.sample

Commenting data lines in .loc.sample tool-data files so tools will not throw exceptions.

2008-04-03 14:31:16 +00:00

faseq.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00

fastx_clipper_sequences.txt

Updating FASTX tool-set to the latest version v0.0.10

2009-09-14 17:03:17 -04:00

lastz_seqs.loc.sample

Fixes for lastz_wrapper that includes job splitting, more functional tests, removed incorrectly committed .loc file and committed the .loc.sample file.

2009-12-01 20:16:41 -05:00

liftOver.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00

maf_index.loc.sample

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

maf_pairwise.loc.sample

Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.

2008-05-29 17:38:46 +00:00

microbial_data.loc.sample

Commenting data lines in .loc.sample tool-data files so tools will not throw exceptions.

2008-04-03 14:31:16 +00:00

perm_base_index.loc.sample

First pass as PerM. Also made cosmetic changes to BWA.

2010-03-17 16:40:36 -04:00

perm_color_index.loc.sample

First pass as PerM. Also made cosmetic changes to BWA.

2010-03-17 16:40:36 -04:00

phastOdds.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00

quality_scores.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00

regions.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00

sam_fa_indices.loc.sample

Updated several sample index loc files to make it clearer how the actual loc files should appear

2009-10-07 15:31:18 -04:00

sequence_index_base.loc.sample

Updated several sample index loc files to make it clearer how the actual loc files should appear

2009-10-07 15:31:18 -04:00

sequence_index_color.loc.sample

Updated several sample index loc files to make it clearer how the actual loc files should appear

2009-10-07 15:31:18 -04:00

twobit.loc.sample

Added more information to the sample .loc files, fixed a typo in extract genomic dna tool.

2008-06-30 18:02:53 +00:00