[Blends-commit] [Git][blends-team/med][master] Fully remove commented entries - we have Git for restoring things if ever needed

Andreas Tille gitlab at salsa.debian.org
Wed Jul 4 20:19:54 BST 2018 

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
cf03a16b by Andreas Tille at 2018-07-04T21:19:27+02:00
Fully remove commented entries - we have Git for restoring things if ever needed

- - - - -


1 changed file:

- tasks/bio


Changes:

=====================================
tasks/bio
=====================================
--- a/tasks/bio
+++ b/tasks/bio
@@ -1257,16 +1257,6 @@ 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).
-#
-# 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
 License: GPL
@@ -1827,151 +1817,6 @@ 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.
-#
-# 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
 
 Recommends: r-cran-ape
@@ -2403,21 +2248,6 @@ Pkg-Description: editor for biological ontologies
  and part-of relations. Amongst the databases cureated by this tool
  is the GeneOntology.
 
-
-#Recommends: jstreeview
-#Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml
-#License: MIT/X11
-#Language: JavaScript
-#Pkg-Description: Editor for Phylogenetic Trees
-# A concise viewer/editor for phylogenetic trees in the Newick format.
-# The core functions are written in JavaScript, using the canvas tag
-# proposed by HTML 5. No server side support is needed for rendering the
-# picture and therefore you can grab this page together with knhx.js and
-# 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
-
 Recommends: phagefinder
 Homepage: http://phage-finder.sourceforge.net/
 License: GPL
@@ -2516,15 +2346,6 @@ Recommends: vcftools
 
 Suggests: mobyle, mobyle-programs, mobyle-tutorials
 
-#Recommends: hilbertvisgui
-#Homepage: http://www.bioconductor.org/help/bioc-views/2.7/bioc/html/HilbertVisGUI.html
-#License: GPL-3
-#Pkg-Description: interactive tool to visualize long vectors of integer data by means of Hilbert curves
-# An interactive tool to visualize long vectors of integer data by means of Hilbert
-# curves.  It provides a GUI for the Debian packaged r-bioc-hilbertvis and is thus
-# interesting for giving users some comfort.  Until this software is not yet packaged
-# you can follow the hint at the homepage how to use it with R.
-
 Recommends: beads
 Pkg-URL: https://launchpad.net/~olivier-langella/+archive/ppa/+packages
 



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