[Blends-commit] [Git][blends-team/med][master] Removed some uninspiring ones from bio.
Steffen Möller
gitlab at salsa.debian.org
Wed Jul 4 16:17:01 BST 2018
Steffen Möller pushed to branch master at Debian Blends Team / med
Commits:
9ba96df3 by Steffen Möller at 2018-07-04T15:16:56+00:00
Removed some uninspiring ones from bio.
- - - - -
1 changed file:
- tasks/bio
Changes:
=====================================
tasks/bio
=====================================
--- a/tasks/bio
+++ b/tasks/bio
@@ -1257,13 +1257,15 @@ Remark: Issuer of previous ITP said:
Probably it makes sense to remove this project from the prospective packages
list.
-Recommends: gbioseq
-Homepage: http://www.bioinformatics.org/project/?group_id=94
-License: GPL
-Pkg-Description: DNA sequence editor for Linux
- gBioSeq is in an early stage of development, but it is already running.
- The goal is to provide an easy to use software to edit DNA sequences under
- Linux, Windows, MacOsX, using GTK C# (Mono).
+#Recommends: gbioseq
+#Homepage: http://www.bioinformatics.org/project/?group_id=94
+#License: GPL
+#Pkg-Description: DNA sequence editor for Linux
+# gBioSeq is in an early stage of development, but it is already running.
+# The goal is to provide an easy to use software to edit DNA sequences under
+# Linux, Windows, MacOsX, using GTK C# (Mono).
+#
+# Update: Still in the early development phase in which Debian does not need it
Recommends: phpphylotree
Homepage: http://www.bioinformatics.org/project/?group_id=372
@@ -1825,137 +1827,150 @@ Pkg-Description: quality-control checking of finished cDNA clone sequences
dump cDNA clones sequences (such as those that passed the QC
checking) from the cdna_db.
-Recommends: das-proserver
-Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/
-License: Same as Perl
-Pkg-Description: lightweight Distributed Annotation System (DAS) server
- The Distributed Annotation System (DAS) is a data exchange protocol
- for open sharing of biological information.
- .
- ProServer is a very lightweight DAS server written in Perl. It is
- simple to install and configure and has existing adaptors for a wide
- variety of data sources. It is also easily extensible allowing
- adaptors to be written for other data sources. More information about
- the DAS protocol and what it is useful for is available over at
- http://biodas.org.
- .
- New large scale techniques in biology are producing a rapidly growing
- amount of public available data. Centralized database resources are
- confronted with the task how to scale their storage facilities, how
- to manage frequent updates and how to exchange the data with the
- community.
- .
- The Distributed Annotation System (DAS) addresses these issues. It is
- frequently being used to openly exchange biological annotations
- between distributed sites. Data distribution, performed by DAS
- servers, is separated from visualization, which is done by DAS
- clients.
- .
- DAS is a client-server system in which a client like Ensembl
- integrates information from multiple servers. It allows a single
- machine to gather up genome annotation information from multiple
- distant web sites, collate the information, and display it to the
- user in a single view. Little coordination is needed among the
- various information providers.
- .
- DAS is heavily used in the genome bioinformatics community. Over the
- last years we have also seen growing acceptance in the protein
- sequence and structure communities.
-
-Recommends: spice
-Homepage: http://www.efamily.org.uk/software/dasclients/spice/
-License: GPL
-Pkg-Description: Distributed Annotation System (DAS) client
- The Distributed Annotation System (DAS) is a data exchange protocol
- for open sharing of biological information.
- .
- SPICE is a browser for protein sequences, structures and their
- annotations. It can display annotations for PDB, UniProt and Ensembl
- Peptides. All data is retrieved from different sites on the Internet,
- that make their annotations available using the DAS protocol. It is
- possible to add new annotations to SPICE, and to compare them with
- the already available information.
-
-Recommends: decipher
-Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/
-License: To be clarified
-Pkg-Description: tracks duplications and deletions of DNA in patients
- DECIPHER tracks submicroscopic duplications and deletions of DNA in
- patients together with phenotypes exhibited by those
- patients. DECIPHER tallies these genetic abnormalities with genes and
- other features of interest in the affected areas. The aim of DECIPHER
- is to provide a research tool to aid clinical diagnosis and treatment
- of these conditions. DECIPHER makes use of DAS technology to
- integrate with Ensembl, the world's leading genome browser.
-
-Recommends: est-db
-Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/
-License: Artistic
-Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
- The est_db package is a software suite and database system designed
- to support expressed sequence tag (EST) sequencing projects, and to
- provide comprehensive bioinformatic analysis of sequenced EST
- libraries, for gene discovery and other purposes. The database can
- hold and efficiently process hundreds of thousands of EST sequences,
- track the cDNA libraries and clones to which they belong, and store
- the results of their analysis. Should they be available, large
- compute farms can be used for the analysis.
- .
- Extensive bioinformatic analysis can be carried out on the sequenced
- EST libraries, including similarity (BLAST) searches, protein
- sequence prediction, and the import of EST clustering and assembly
- data from external sources. Results are searchable via a web page,
- with graphic output of the various analyses, enabling one to retrieve
- information pertaining to a particular cDNA clone, or EST read, as
- well as view EST clustering results, or graphical representations of
- BLAST results on the searched EST sequences.
- .
- The est_db package is likely to appeal not only to sequencing groups
- directly employed in EST sequencing, but also to groups interested in
- performing bespoke analysis of ESTs that may already be publically
- available, in order to support their ongoing research aims. The
- package is easily-extensible, via an API designed specifically to
- handle ESTs and their analysis. It is open source and is made
- available free of charge, and, where possible, similarly
- open-licensed components have been used in its development.
-
-Recommends: finex
-Homepage: http://www.sanger.ac.uk/Software/analysis/finex/
-License: To be clarified
-Pkg-Description: sequence homology searching
- The FINEX program allows sequence homology searching techniques to be
- applied, where the sequence data is replaced with a fingerprint
- abstracted from the intron/exon boundary phase and the exon length.
- .
- Please note FINEX is no longer supported but is available for
- download.
-
-Recommends: hexamer
-Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/
-License: GPL
-Pkg-Description: scan DNA sequences to look for likely coding regions
- Hexamer is a program to scan DNA sequences to look for likely coding
- regions. The principle is to use 6mers, but to avoid deriving any
- information from base composition. Therefore, the frequencies of each
- 6mer are normalized by dividing by the total frequency of all 6mers
- with the same base composition.
- .
- There are two programs involved in this process:
- * hextable
- hextable makes files of statistics that hexamer uses to scan for
- likely coding regions.
- The input of hextable is a fasta file of coding sequences in
- frame. The -o file output is an ascii list of 4096 floating point
- numbers giving log likelihood ratio scores in bits. The output on
- stdout is a summary of the information content of the table,
- indicating how disriminative it is likely to be.
- * hexamer
- Uses the .hex file from hextable to scan a DNA sequence for likely
- coding regions.
- The input is a fasta DNA file (n.b. that these programs assume all
- 'a','c','g','t'. 'n's found in the sequence files will be
- converted to 'c'.
- The output of hexamer is in General Feature Format (GFF) format.
+#Recommends: das-proserver
+#Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/
+#License: Same as Perl
+#Pkg-Description: lightweight Distributed Annotation System (DAS) server
+# The Distributed Annotation System (DAS) is a data exchange protocol
+# for open sharing of biological information.
+# .
+# ProServer is a very lightweight DAS server written in Perl. It is
+# simple to install and configure and has existing adaptors for a wide
+# variety of data sources. It is also easily extensible allowing
+# adaptors to be written for other data sources. More information about
+# the DAS protocol and what it is useful for is available over at
+# http://biodas.org.
+# .
+# New large scale techniques in biology are producing a rapidly growing
+# amount of public available data. Centralized database resources are
+# confronted with the task how to scale their storage facilities, how
+# to manage frequent updates and how to exchange the data with the
+# community.
+# .
+# The Distributed Annotation System (DAS) addresses these issues. It is
+# frequently being used to openly exchange biological annotations
+# between distributed sites. Data distribution, performed by DAS
+# servers, is separated from visualization, which is done by DAS
+# clients.
+# .
+# DAS is a client-server system in which a client like Ensembl
+# integrates information from multiple servers. It allows a single
+# machine to gather up genome annotation information from multiple
+# distant web sites, collate the information, and display it to the
+# user in a single view. Little coordination is needed among the
+# various information providers.
+# .
+# DAS is heavily used in the genome bioinformatics community. Over the
+# last years we have also seen growing acceptance in the protein
+# sequence and structure communities.
+#
+# Update: All once true - upstream seems dead, though.
+
+#Recommends: spice
+#Homepage: http://www.efamily.org.uk/software/dasclients/spice/
+#License: GPL
+#Pkg-Description: Distributed Annotation System (DAS) client
+# The Distributed Annotation System (DAS) is a data exchange protocol
+# for open sharing of biological information.
+# .
+# SPICE is a browser for protein sequences, structures and their
+# annotations. It can display annotations for PDB, UniProt and Ensembl
+# Peptides. All data is retrieved from different sites on the Internet,
+# that make their annotations available using the DAS protocol. It is
+# possible to add new annotations to SPICE, and to compare them with
+# the already available information.
+#
+# Update: Would be interesting to have, but not of "reddish" importance for
+# for Debian to redistribute.
+
+#Recommends: decipher
+#Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/
+#License: To be clarified
+#Pkg-Description: tracks duplications and deletions of DNA in patients
+# DECIPHER tracks submicroscopic duplications and deletions of DNA in
+# patients together with phenotypes exhibited by those
+# patients. DECIPHER tallies these genetic abnormalities with genes and
+# other features of interest in the affected areas. The aim of DECIPHER
+# is to provide a research tool to aid clinical diagnosis and treatment
+# of these conditions. DECIPHER makes use of DAS technology to
+# integrate with Ensembl, the world's leading genome browser.
+#
+# No longer available upstream. Decipher is a project at the
+# Sanger Center, though: https://decipher.sanger.ac.uk that redistributes
+# a data source.
+
+#Recommends: est-db
+#Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/
+#License: Artistic
+#Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
+# The est_db package is a software suite and database system designed
+# to support expressed sequence tag (EST) sequencing projects, and to
+# provide comprehensive bioinformatic analysis of sequenced EST
+# libraries, for gene discovery and other purposes. The database can
+# hold and efficiently process hundreds of thousands of EST sequences,
+# track the cDNA libraries and clones to which they belong, and store
+# the results of their analysis. Should they be available, large
+# compute farms can be used for the analysis.
+# .
+# Extensive bioinformatic analysis can be carried out on the sequenced
+# EST libraries, including similarity (BLAST) searches, protein
+# sequence prediction, and the import of EST clustering and assembly
+# data from external sources. Results are searchable via a web page,
+# with graphic output of the various analyses, enabling one to retrieve
+# information pertaining to a particular cDNA clone, or EST read, as
+# well as view EST clustering results, or graphical representations of
+# BLAST results on the searched EST sequences.
+# .
+# The est_db package is likely to appeal not only to sequencing groups
+# directly employed in EST sequencing, but also to groups interested in
+# performing bespoke analysis of ESTs that may already be publically
+# available, in order to support their ongoing research aims. The
+# package is easily-extensible, via an API designed specifically to
+# handle ESTs and their analysis. It is open source and is made
+# available free of charge, and, where possible, similarly
+# open-licensed components have been used in its development.
+#
+# No longer available upstream.
+
+#Recommends: finex
+#Homepage: http://www.sanger.ac.uk/Software/analysis/finex/
+#License: To be clarified
+#Pkg-Description: sequence homology searching
+# The FINEX program allows sequence homology searching techniques to be
+# applied, where the sequence data is replaced with a fingerprint
+# abstracted from the intron/exon boundary phase and the exon length.
+# .
+# Please note FINEX is no longer supported but is available for
+# download.
+#Update: It is no longer available for download, either.
+
+#Recommends: hexamer
+#Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/
+#License: GPL
+#Pkg-Description: scan DNA sequences to look for likely coding regions
+# Hexamer is a program to scan DNA sequences to look for likely coding
+# regions. The principle is to use 6mers, but to avoid deriving any
+# information from base composition. Therefore, the frequencies of each
+# 6mer are normalized by dividing by the total frequency of all 6mers
+# with the same base composition.
+# .
+# There are two programs involved in this process:
+# * hextable
+# hextable makes files of statistics that hexamer uses to scan for
+# likely coding regions.
+# The input of hextable is a fasta file of coding sequences in
+# frame. The -o file output is an ascii list of 4096 floating point
+# numbers giving log likelihood ratio scores in bits. The output on
+# stdout is a summary of the information content of the table,
+# indicating how disriminative it is likely to be.
+# * hexamer
+# Uses the .hex file from hextable to scan a DNA sequence for likely
+# coding regions.
+# The input is a fasta DNA file (n.b. that these programs assume all
+# 'a','c','g','t'. 'n's found in the sequence files will be
+# converted to 'c'.
+# The output of hexamer is in General Feature Format (GFF) format.
+# No longer available for download.
Recommends: coot
@@ -2075,8 +2090,11 @@ Pkg-Description: processes, clusters and annotates EST data
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
Recommends: lamarc
+Homepage: http://evolution.genetics.washington.edu/lamarc/index.html
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html.
+ In 1/2018 upstream has apparently updated their tarball to help the
+ redistribution of their software. Someone please go for it.
Recommends: lucy
Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
View it on GitLab: https://salsa.debian.org/blends-team/med/commit/9ba96df3ed031325b5ec50bba31dc5ee36adaabc
--
View it on GitLab: https://salsa.debian.org/blends-team/med/commit/9ba96df3ed031325b5ec50bba31dc5ee36adaabc
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/blends-commit/attachments/20180704/7ca55a08/attachment-0001.html>
More information about the Blends-commit
mailing list