[Blends-commit] r2614 - /projects/med/trunk/debian-med/tasks/bio

Thu Jan 20 17:14:01 UTC 2011

Author: tille
Date: Thu Jan 20 17:14:00 2011
New Revision: 2614

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2614
Log:
Added sra-sdk

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2614&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Thu Jan 20 17:14:00 2011
@@ -126,7 +126,7 @@
 Depends: poa
 Published-Authors: C. Grasso, C. Lee
 Published-Title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
-Published-In: Bioinformatics 20(10):1546-1556. 
+Published-In: Bioinformatics 20(10):1546-1556.
 Published-Year: 2004
 
 Depends: probcons
@@ -169,7 +169,7 @@
 Depends: clustalw
 Published-Authors: M. Larkin, et al.
 Published-Title: Clustal W and Clustal X version 2.0
-Published-In: Bioinformatics 23(21):2947-2948 
+Published-In: Bioinformatics 23(21):2947-2948
 Published-Year: 2007
 
 Depends: clustalw-mpi
@@ -269,7 +269,7 @@
 Depends:     glam2
 Why:         Motif search
 Published-Title: Discovering sequence motifs with arbitrary insertions and deletions
-Published-Authors: MC Frith, NFW Saunders, B Kobe, TL Bailey 
+Published-Authors: MC Frith, NFW Saunders, B Kobe, TL Bailey
 Published-In: PLoS Computational Biology
 Published-Year: 2008
 Published-DOI: 10.1371/journal.pcbi.1000071
@@ -326,7 +326,7 @@
 
 Depends: r-bioc-hilbertvis
 Published-Authors: Simon Anders
-Published-Title: Visualization of genomic data with the Hilbert curve 
+Published-Title: Visualization of genomic data with the Hilbert curve
 Published-In: Bioinformatics 25(10):1231-1235
 Published-Year: 2009
 Published-DOI: 10.1093/bioinformatics/btp152
@@ -361,7 +361,7 @@
 Published-Year: 2006
 Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16837528
 Published-DOI: 10.1093/bioinformatics/btl369
-Published-PubMed: 16837528 
+Published-PubMed: 16837528
 
 Suggests: seqan-apps
 
@@ -370,8 +370,8 @@
 Depends: gentle
 
 Depends: gmap
-Published-Title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences  
-Published-Authors: Thomas D. Wu, Colin K. Watanabe 
+Published-Title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences
+Published-Authors: Thomas D. Wu, Colin K. Watanabe
 Published-In: Bioinformatics
 Published-Year: 2005
 Published-URL: http://bioinformatics.oupjournals.org/cgi/content/full/21/9/1859
@@ -3065,7 +3065,7 @@
  canvastext.js to locally view your trees in a supported web browser.
  .
  The source can be downloaded at
- http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip                    
+ http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip
 
 Depends: phagefinder
 Homepage: http://phage-finder.sourceforge.net/
@@ -3195,7 +3195,7 @@
  accelerate the computation with many nodes. The pipeline can accurately analyze
  over 35x coverage of a human genome in one day on a 10-node local cluster, or
  in 3 hours for about $100 using a 40-node, 320-core cluster rented from
- Amazon's EC2 utility computing service. 
+ Amazon's EC2 utility computing service.
 Published-Title: Searching for SNPs with cloud computing
 Published-Authors: Ben Langmead, Michael Schatz, Jimmy Lin, Mihai Pop, Steven Salzberg
 Published-In: Genome Biology
@@ -3305,15 +3305,15 @@
  for the Maq alignment file and allows you to see the mismatches, base
  qualities and mapping qualities. Maqview is nothing fancy as Consed or
  GAP, but just a simple viewer for you to see what happens in a
- particular region.             
+ particular region.
  .
  In comparison to tgap-maq, the text-based read alignment viewer writen
  by James Bonfield, Maqview is faster and takes up much less memory and
- disk space in indexing. This is possibly because tgap aims to be a 
- general-purpose viewer but Maqview fully makes use of the fact that a 
+ disk space in indexing. This is possibly because tgap aims to be a
+ general-purpose viewer but Maqview fully makes use of the fact that a
  Maq alignment file has already been sorted. Maqview is also efficient in
  viewing and provides a command-line tool to quickly retrieve any region
- in an Maq alignment file.       
+ in an Maq alignment file.
  .
  Maqview is based on OpenGL. Installing OpenGL on your system is the                                       trade-off of getting a better feel and look. The following screenshots
  show the two viewing modes of Maqview.
@@ -3363,19 +3363,46 @@
 Responsible: Olivier Sallou <olivier.sallou at irisa.fr>
 Language: Java
 Pkg-Description: Biological banks updater
- BioMAJ downloads remote biological data banks, check their status and 
- apply transformation workflows, with consistent state, to provide 
+ BioMAJ downloads remote biological data banks, check their status and
+ apply transformation workflows, with consistent state, to provide
  ready-to-use data to biologists and bioinformaticians.
- For example, it can transform original fasta files to blast indexes. It 
+ For example, it can transform original fasta files to blast indexes. It
  is very flexible and post-processes can be extended very easily.
  .
- BioMAJ includes some post-processes and bank properties (genbank, uniprot 
+ BioMAJ includes some post-processes and bank properties (genbank, uniprot
  ...).
  .
  A web administration interface is provided.
 Remark: Similar to getData
  Steffen MÃ¶ller stated that the project is similar to http://wiki.debian.org/getData
 
+Depends: sra-sdk
+Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software
+License: Public domain (U. S. A. governmental work)
+WNPP: 610603
+Responsible: Charles Plessy <plessy at debian.org>
+Programming Lang: C
+Description: utilities for the NCBI Sequence Read Archive
+ Tools for reading the SRA archive, generally by converting individual runs
+ into some commonly used format such as fastq. It also includes sources to
+ loader tools that are still under test. The intention is to give pre-release
+ access to the reader code.
+ .
+ The textual dumpers "sra-dump" and "vdb-dump" are provided in this
+ release as an aid in visual inspection. It is likely that their
+ actual output formatting will be changed in the near future to a
+ stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON
+ THE OUTPUT FORMAT SEEN IN THIS RELEASE.
+ .
+ The "help" information will be improved in near future releases, and
+ the tool options will become standardized across the set. We will
+ also be providing documentation on our web site.
+ .
+ Tool options may change in the next release. Version 1 tool options
+ will remain supported wherever possible in order to preserve
+ operation of any existing scripts.
+
+
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html


