[Blends-commit] r2836 - in /projects/med/trunk/debian-med/tasks: bio imaging
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Wed Jun 8 06:45:18 UTC 2011
Author: tille
Date: Wed Jun 8 06:45:18 2011
New Revision: 2836
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2836
Log:
Some Vcs-fields, added bedtools, removed useless whitespaces
Modified:
projects/med/trunk/debian-med/tasks/bio
projects/med/trunk/debian-med/tasks/imaging
Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2836&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed Jun 8 06:45:18 2011
@@ -3077,11 +3077,11 @@
Published-URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
Published-Year: 2010
-Depends: ncbi-blast-plus
+Depends: ncbi-blast+
License: BSD
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast-plus/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-blast-plus/?rev=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast+/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-blast+/?rev=0
WNPP: 150636
Pkg-Description: NCBI Blast+ is new blast evolution
The Basic Local Alignment Search Tool (BLAST) is the most widely
@@ -3438,7 +3438,7 @@
Users can either specify fields, or logical combinations of fields to
flexibly filter datasets on the fly. Users can compare multiple datasets
at various functional and taxonomic levels applying statistical tests as
- well as hierarchical clustering, multidimensional scaling and heatmaps.
+ well as hierarchical clustering, multidimensional scaling and heatmaps.
Depends: smalt
License: "shortly" under GPL
@@ -3461,7 +3461,7 @@
of the hashed words.
.
A mode for the detection of split (chimeric) reads is provided.
- Multi-threaded program execution is supported.
+ Multi-threaded program execution is supported.
Remark: This can be regarded as successor of ssaha2
This program is from the same author as ssaha2 and according to its author
faster and more precise than ssaha2 (except for sequences > 2000bp).
@@ -3490,7 +3490,7 @@
VCFtools is a program package designed for working with VCF files, such
as those generated by the 1000 Genomes Project. The aim of VCFtools is
to provide methods for working with VCF files: validating, merging,
- comparing and calculate some basic population genetic statistics.
+ comparing and calculate some basic population genetic statistics.
Remark: Packaging requested by BIOLINUX
This package is listed at http://www.bioinformatics.org/wiki/BIOLINUX to
be quite important for BIOLINUX.
@@ -3521,7 +3521,7 @@
2000. It began with the classic "overlap-layout-consensus" paradigm and
has since developed into a vast collection of tools, implemented in
numerous modules, to analyze, visualize and manipulate assemblies. New
- and improved algorithms are becoming available on a regular basis.
+ and improved algorithms are becoming available on a regular basis.
Depends: maker2
Homepage: http://www.yandell-lab.org/software/maker.html
@@ -3557,50 +3557,50 @@
Homepage: http://www.repeatmasker.org/
License: Open Software License v. 2.1
Pkg-Description: screens DNA sequences for interspersed repeats
- RepeatMasker is a program that screens DNA sequences for interspersed
- repeats and low complexity DNA sequences. The output of the program is a detailed
- annotation of the repeats that are present in the query sequence as well as a
- modified version of the query sequence in which all the annotated repeats have
- been masked (default: replaced by Ns). On average, almost 50% of a human genomic
- DNA sequence currently will be masked by the program. Sequence comparisons in
- RepeatMasker are performed by one of several popular search engines including,
+ RepeatMasker is a program that screens DNA sequences for interspersed
+ repeats and low complexity DNA sequences. The output of the program is a detailed
+ annotation of the repeats that are present in the query sequence as well as a
+ modified version of the query sequence in which all the annotated repeats have
+ been masked (default: replaced by Ns). On average, almost 50% of a human genomic
+ DNA sequence currently will be masked by the program. Sequence comparisons in
+ RepeatMasker are performed by one of several popular search engines including,
cross_match, ABBlast/WUBlast, RMBlast and Decypher.
Depends: trf
Homepage: http://tandem.bu.edu/trf/trf.html
License: binary only (non-free)
Pkg-Description: Tandem Repeats Finder
- A tandem repeat in DNA is two or more adjacent, approximate copies of a
- pattern of nucleotides. Tandem Repeats Finder is a program to locate and
- display tandem repeats in DNA sequences. In order to use the program, the
- user submits a sequence in FASTA format. There is no need to specify the
- pattern, the size of the pattern or any other parameter. The output consists
- of two files: a repeat table file and an alignment file. The repeat table
- contains information about each repeat, including its location, size,
- number of copies and nucleotide content. Clicking on the location indices
- for one of the table entries opens a second web browser that shows an
- alignment of the copies against a consensus pattern. The program is very
- fast, analyzing sequences on the order of .5Mb in just a few seconds.
- Submitted sequences may be of arbitrary length. Repeats with pattern size
- in the range from 1 to 2000 bases are detected. Sequence information sent
+ A tandem repeat in DNA is two or more adjacent, approximate copies of a
+ pattern of nucleotides. Tandem Repeats Finder is a program to locate and
+ display tandem repeats in DNA sequences. In order to use the program, the
+ user submits a sequence in FASTA format. There is no need to specify the
+ pattern, the size of the pattern or any other parameter. The output consists
+ of two files: a repeat table file and an alignment file. The repeat table
+ contains information about each repeat, including its location, size,
+ number of copies and nucleotide content. Clicking on the location indices
+ for one of the table entries opens a second web browser that shows an
+ alignment of the copies against a consensus pattern. The program is very
+ fast, analyzing sequences on the order of .5Mb in just a few seconds.
+ Submitted sequences may be of arbitrary length. Repeats with pattern size
+ in the range from 1 to 2000 bases are detected. Sequence information sent
to the server is confidential and deleted after program execution.
Published-Title: Tandem repeats finder: a program to analyze DNA sequences
Published-Authors: G. Benson
Published-In: Nucleic Acids Research
Published-Year: 1999
-Depends: rmblast
+Depends: rmblast
Homepage: http://tandem.bu.edu/trf/trf.html
License: Same as blast2
Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST
- RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST
- suite. The primary difference between this distribution and the NCBI
- distribution is the addition of a new program "rmblastn" for use with
- RepeatMasker and RepeatModeler.
- RMBlast supports RepeatMasker searches by adding a few necessary features
- to the stock NCBI blastn program. These include: Support for custom matrices
- ( without KA-Statistics ). Support for cross_match-like complexity adjusted
- scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
+ RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST
+ suite. The primary difference between this distribution and the NCBI
+ distribution is the addition of a new program "rmblastn" for use with
+ RepeatMasker and RepeatModeler.
+ RMBlast supports RepeatMasker searches by adding a few necessary features
+ to the stock NCBI blastn program. These include: Support for custom matrices
+ ( without KA-Statistics ). Support for cross_match-like complexity adjusted
+ scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
Support for cross_match-like masklevel filtering.
Depends: augustus
@@ -3608,22 +3608,22 @@
License: not explicitely specified
Pkg-Description: predict genes in eukaryotic genomic sequences
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
- It can be run on this web server or be downloaded and run locally. It is
- open source so you can compile it for your computing platform. You can now
- run AUGUSTUS on the German MediGRID. This enables you to submit larger
- sequence files and allows to use protein homology information in the
- prediction. The MediGRID requires an instant easy registration by email
+ It can be run on this web server or be downloaded and run locally. It is
+ open source so you can compile it for your computing platform. You can now
+ run AUGUSTUS on the German MediGRID. This enables you to submit larger
+ sequence files and allows to use protein homology information in the
+ prediction. The MediGRID requires an instant easy registration by email
for first-time users.
-
+
Depends: mugsy
Homepage: http://mugsy.sourceforge.net/
License: Artistic License 2.0
Pkg-Description: multiple whole genome aligner
- Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise
- alignment, a custom graph based segmentation procedure for identifying
- collinear regions, and the segment-based progressive multiple alignment
- strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form
- of multi-FASTA files and does not require a reference genome.
+ Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise
+ alignment, a custom graph based segmentation procedure for identifying
+ collinear regions, and the segment-based progressive multiple alignment
+ strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form
+ of multi-FASTA files and does not require a reference genome.
Published-Title: Mugsy: fast multiple alignment of closely related whole genomes
Published-Authors: Angiuoli SV, Salzberg SL
Published-In: Bioinformatics
@@ -3633,18 +3633,18 @@
Homepage: http://gmod.org/wiki/Apollo
License: Artistic License
Pkg-Description: genome annotation viewer and editor
- Apollo is a genome annotation viewer and editor. It was developed as a
- collaboration between the Berkeley Drosophila Genome Project (part of
- the FlyBase consortium) and The Sanger Institute in Cambridge, UK.
- Apollo allows researchers to explore genomic annotations at many levels
- of detail, and to perform expert annotation curation, all in a graphical
- environment. It was used by the FlyBase biologists to construct the
- Release 3 annotations on the finished Drosophila melanogaster genome,
- and is also a primary vehicle for sharing these annotations with the
- community. The Generic Model Organism Database (GMOD) project, which
- aims to provide a complete ready-to-use toolkit for analyzing whole
- genomes, has adopted Apollo as its annotation workbench. Apollo is a
- Java application that can be downloaded and run on Windows, Mac OS X,
+ Apollo is a genome annotation viewer and editor. It was developed as a
+ collaboration between the Berkeley Drosophila Genome Project (part of
+ the FlyBase consortium) and The Sanger Institute in Cambridge, UK.
+ Apollo allows researchers to explore genomic annotations at many levels
+ of detail, and to perform expert annotation curation, all in a graphical
+ environment. It was used by the FlyBase biologists to construct the
+ Release 3 annotations on the finished Drosophila melanogaster genome,
+ and is also a primary vehicle for sharing these annotations with the
+ community. The Generic Model Organism Database (GMOD) project, which
+ aims to provide a complete ready-to-use toolkit for analyzing whole
+ genomes, has adopted Apollo as its annotation workbench. Apollo is a
+ Java application that can be downloaded and run on Windows, Mac OS X,
or any Unix-type system (including Linux).
Published-Title: Apollo: a sequence annotation editor
Published-Authors: Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME
@@ -3657,7 +3657,7 @@
Pkg-Description: distributed processing system based on 'autonomous agents'
This is a distributed processing system based on 'autonomous agents' and
Hive behavioural structure of Honey Bees . It implements all functionality
- of both data-flow graphs and block-branch diagrams which should allow it
+ of both data-flow graphs and block-branch diagrams which should allow it
to codify any program, algorithm, or parallel processing job control system.
It is not bound to any processing 'farm' system and can be adapted to any GRID.
@@ -3665,9 +3665,9 @@
Homepage: http://gmod.org/wiki/Chado
License: Not specified
Pkg-Description: relational database schema for data frequently encountered in modern biology
- Chado is a relational database schema that underlies many GMOD installations.
- It is capable of representing many of the general classes of data frequently
- encountered in modern biology such as sequence, sequence comparisons,
+ Chado is a relational database schema that underlies many GMOD installations.
+ It is capable of representing many of the general classes of data frequently
+ encountered in modern biology such as sequence, sequence comparisons,
phenotypes, genotypes, ontologies, publications, and phylogeny. It has been
designed to handle complex representations of biological knowledge and should
be considered one of the most sophisticated relational schemas currently
@@ -3684,42 +3684,42 @@
Homepage: http://gmod.org/wiki/GBrowse_syn
License: Not specified
Pkg-Description: Generic Synteny Browser
- GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny
- browser designed to display multiple genomes, with a central reference
- species compared to two or more additional species. It can be used to
- view multiple sequence alignment data, synteny or co-linearity data
- from other sources against genome annotations provided by GBrowse.
- GBrowse_syn is included with the standard GBrowse package (version 1.69 and
+ GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny
+ browser designed to display multiple genomes, with a central reference
+ species compared to two or more additional species. It can be used to
+ view multiple sequence alignment data, synteny or co-linearity data
+ from other sources against genome annotations provided by GBrowse.
+ GBrowse_syn is included with the standard GBrowse package (version 1.69 and
later). Working examples can be seen at TAIR and WormBase.
Depends: jbrowse
Homepage: http://gmod.org/wiki/JBrowse
License: Not specified
Pkg-Description: genome browser with an AJAX-based interface
- JBrowse is a genome browser with an AJAX-based interface. JBrowse renders most
- tracks using client side JavaScript and JSON as its data transfer format.
+ JBrowse is a genome browser with an AJAX-based interface. JBrowse renders most
+ tracks using client side JavaScript and JSON as its data transfer format.
JBrowse is the official successor to GBrowse.
Depends: tripal
Homepage: http://www.genome.clemson.edu/software/tripal
License: GPL ( as Drupal a derivative )
Pkg-Description: collection of Drupal modules for genomic research
- Tripal is a collection of open-source freely available Drupal modules under
- development at CUGI and a member of the GMOD family of tools. Tripal serve
- as a web interface for the GMOD Chado database. Tripal intially started as
- a web front-end for the Marine Genomics Project (MG.org). Work on the
- interface is currently ongoing for the MG.org project as well as the
- Fagaceae Genomics Web, and other CUGI projects. Tripal is currently being
- implemented for the new Cacao Genome Database, and Citrus Genome Database
- and will be used for the Genome Database for Rosaceae. These latter three
- databases are projects of the Main Bioinformatics Laboratory at Washington
+ Tripal is a collection of open-source freely available Drupal modules under
+ development at CUGI and a member of the GMOD family of tools. Tripal serve
+ as a web interface for the GMOD Chado database. Tripal intially started as
+ a web front-end for the Marine Genomics Project (MG.org). Work on the
+ interface is currently ongoing for the MG.org project as well as the
+ Fagaceae Genomics Web, and other CUGI projects. Tripal is currently being
+ implemented for the new Cacao Genome Database, and Citrus Genome Database
+ and will be used for the Genome Database for Rosaceae. These latter three
+ databases are projects of the Main Bioinformatics Laboratory at Washington
State University
Depends: genemark
Homepage: http://exon.biology.gatech.edu/
License: Academic License Agreement
Pkg-Description: family of gene prediction programs
- A family of gene prediction programs developed at Georgia Institute of
+ A family of gene prediction programs developed at Georgia Institute of
Technology, Atlanta, Georgia, USA.
Depends: strap
@@ -3739,7 +3739,7 @@
right mouse click. The program appears to be complicated in the
beginning. With the help of the integrated tutorials you will learn how
to apply the currently available methods to compare proteins sequences
- and structures.
+ and structures.
.
Key features are:
* Visualization and manipulation of sequence alignments (up to 1000
@@ -3754,7 +3754,20 @@
* High quality PDF output by LaTeX/TeXshade
* Project safety by included backup system
* Translation of nucleotide sequences to amino acid sequences
- * Residue selections
+ * Residue selections
+
+Depends: bedtools
+License: GPL-2+
+Homepage: http://code.google.com/p/bedtools/
+WNPP: 629597
+Vcs-Git: http://git.debian.org/?p=debian-med/bedtools.git
+Language: C++
+Pkg-Description: suite of utilities for comparing genomic features
+ The BEDTools utilities allow one to address common genomics tasks such as
+ finding feature overlaps and computing coverage. The utilities are largely
+ based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
+ BEDTools, one can develop sophisticated pipelines that answer complicated
+ research questions by streaming several BEDTools together.
Comment: Several related R packages are listed at CRAN:
Modified: projects/med/trunk/debian-med/tasks/imaging
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/imaging?rev=2836&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging (original)
+++ projects/med/trunk/debian-med/tasks/imaging Wed Jun 8 06:45:18 2011
@@ -1186,6 +1186,8 @@
Homepage: http://plastimatch.org/
License: BSD-like
WNPP: 629344
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/plastimatch/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plastimatch/trunk/?rev=0&sc=0
Responsible: Greg Sharp <gregsharp.geo at yahoo.com>
Pkg-Description: high-performance volumetric registration of medical images
Plastimatch is an open source software for deformable image
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