[Blends-commit] [SCM] med branch, master, updated. 20e937635d6d12b2f6ec7a0e1babcb7c63e15ea8
Andreas Tille
tille at debian.org
Sat Aug 22 21:34:38 UTC 2015
The following commit has been merged in the master branch:
commit 20e937635d6d12b2f6ec7a0e1babcb7c63e15ea8
Author: Andreas Tille <tille at debian.org>
Date: Sat Aug 22 23:34:23 2015 +0200
s/^Note:/Remark:/
diff --git a/tasks/bio b/tasks/bio
index edca255..7b0ab01 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -735,7 +735,7 @@ Depends: vmd
Depends: vsearch
Depends: wgs-assembler
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
Depends: wgsim
@@ -984,7 +984,7 @@ Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov
approximate alignment scores efficiently. More detailed information
on the architecture of this system will be made available soon.
Slides from a talk at Computational Genomics 2004 are now available.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
Depends: rose
Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
@@ -1003,7 +1003,7 @@ Pkg-Description: Region-Of-Synteny Extractor
by default) on either side of that region. When a predicted gene
overlaps an alignment we use the gene prediction to extend the
boundaries of the output region.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
Depends: glimmerhmm
Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
@@ -1018,7 +1018,7 @@ Pkg-Description: Eukaryotic Gene-Finding System
structure includes introns of each phase, intergenic regions, and
four types of exons (initial, internal, final, and single). A basic
user manual can be consulted here.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
Depends: genezilla
Homepage: http://www.genezilla.org/
@@ -1048,7 +1048,7 @@ Pkg-Description: eukaryotic gene finder
at The Institute for Genomic Research over a 3-year period under NIH
grants R01-LM06845 and R01-LM007938, and which served as the basis
for the comparative gene finder TWAIN.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
Depends: exalt
Homepage: http://www.cbcb.umd.edu/software/exalt/
@@ -1062,7 +1062,7 @@ Pkg-Description: phylogenetic generalized hidden Markov model for predicting alt
when only a single genomic sequence is available. ExAlt has been
extensively tested on Drosophila melanogaster, but can be adapted to
run on other species.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
Depends: jigsaw
Homepage: http://www.cbcb.umd.edu/software/jigsaw/
@@ -1090,7 +1090,7 @@ Pkg-Description: gene prediction using multiple sources of evidence
viewable as custom tracks in the UCSC Human Genome
Browser. Predictions available for the Human genome and viewable as
custom tracks in the UCSC Human Genome Browser
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
Depends: genesplicer
Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
@@ -1107,7 +1107,7 @@ Pkg-Description: computational method for splice site prediction
There is no independent program to train GeneSplicer, but there is a
way to obtain the necessary files by using the training procedure of
GlimmerHMM.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
Ignore: riso
Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
@@ -1162,7 +1162,7 @@ Pkg-Description: High-throughput sequence alignment using Graphics Processing Un
3.5-fold in total application time when aligning reads from recent
sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
technologies.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
Depends: amoscmp
Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
@@ -1191,7 +1191,7 @@ Pkg-Description: comparative genome assembly package
AMOScmp is part of the AMOS package (see
http://amos.sourceforge.net/)- a collaborative effort to develop a
modular open-source framework for assembly development.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
Depends: minimus
Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
@@ -1224,7 +1224,7 @@ Pkg-Description: AMOS lightweight assembler
.
minimus is part of the AMOS package - a collaborative effort to
develop a modular open-source framework for assembly development.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
Ignore: catissuecore
Homepage: https://cabig.nci.nih.gov/tools/catissuecore
@@ -1240,7 +1240,7 @@ Pkg-Description: biospecimen inventory, tracking, and basic annotation
.
Intended Audiences: Translational Researchers, Pathologists, Biobank
Managers
-Note: A lot of stuff can be found at National Cancer Institute's
+Remark: A lot of stuff can be found at National Cancer Institute's
Center for Bioinformatics (NCICB) Open Source Project Site
http://gforge.nci.nih.gov/ which has to be evaluated and put into the
right category of our tasks files
@@ -1282,7 +1282,7 @@ Pkg-Description: Transcript Annotation Prioritization and Screening System
students Steven Davis and Brian O'Leary has demonstrated the
advantage of the parallel screening method over the sequential
sequencing of large candidate lists.
-Note: Found at
+Remark: Found at
http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
Depends: bambus
@@ -1298,7 +1298,7 @@ Pkg-Description: hierarchical approach to building contig scaffolds
.
Note that currently Bambus is undergoing a transition in order to be
integrated with the AMOS package (see http://amos.sourceforge.net/)
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
Depends: gmv
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
@@ -1326,7 +1326,7 @@ Pkg-Description: novel vector trimming software
DNA words are most likely associated with vector sequence. For a
description of Figaro's algorithms please see our paper. Figaro is
part of the AMOS suite.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
Depends: mirbase
Homepage: http://microrna.sanger.ac.uk/
@@ -1367,7 +1367,7 @@ Pkg-Description: motif finder that can find ribosome binding sites, exon splicin
An online tool that uses ELPH output for identifying exon splicing
enhancers can be found at
http://www.cbcb.umd.edu/software/SeeEse/index.html .
-Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
X-Depends: repeatfinder
X-Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
@@ -1443,7 +1443,7 @@ Pkg-Description: detect and analyze conserved gene pairs
.
OperonDB was supported by the NIH under grant R01-LM007938 and by the
NSF under grant DBI-0234704.
-Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
+Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
no info about license or downloadable code found, but tried to
contact authors.
--
Debian Med metapackages
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