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1.9.5 (2013-10-21)
==================
- update bootstrap.py from ttp://downloads.buildout.org/1/bootstrap.py
- Upgrade to grape.recipe.pipeline 1.1.16
- Better error message when the type parameter in the accession is neither fastq nor bam
1.9.4 (2013-02-13)
==================
- Upgrade to grape.recipe.pipeline 1.1.15
- Make TEMPLATE parameter optional
- Detect wrong template for fastq and bam files
1.9.3 (2013-02-12)
==================
- Use a single bootstrap.py, and update the documentation
- Update bootstrap.py for the latest version of zc.buildout
- Fix configuration checks for bam files
- grape.recipe.pipeline == 1.1.14
- Upgrade to allow plus sign in parameter values
- raisin.pyramid = 1.2.1
- raisin.resource = 1.4.1
1.9.2 (2013-01-09)
==================
- Upgrade to pipeline 6.5.3
- Upgrape to recipe.pipeline version 1.1.13
1.9.1 (2012-12-09)
==================
- Upgrade to pipeline version 6.5.2
1.9 (2012-11-11)
================
- Servers now have a project_downloads and project_downloads_folder
section that can be configured in servers/devel/buildout.cfg
- Use new package versions for the pipelines:
- Grape pipeline version 6.5.1
- grape.recipe.pipeline 1.1.12
- Use new package versions for the servers:
- raisin.recipe.extract version 1.1.3
- raisin.recipe.server version 1.1.7
- raisin.box version 1.4
- raisin.resource version 1.4
- raisin.restish version 1.3
- raisin.restyler version 1.3
- grape.recipe.pipeline version 1.1.12
1.8 (2012-10-09)
================
- Use new Cufflinks, version 2.0.2
- Upgrade to Grape pipeline 6.5
- Allow for the running of the start script with only species, genome, annotation
and read length specified appart from a list of one or two files.
- Set the number of CPUs used by fastqc to one.
- new dependency on grape.recipe.pipeline to share validation code with the Raisin
- Fix a bug that prevented the correct running of the Flux when the read Ids
came from HiSeq
- Add verbose to the mysqlimport statement in the build_exon_junctions.RNAseq.pl
- Install the pre version of GEM in grape.recipe.pipeline 1.1.9, with binaries prefixed
with "next".
- Download packages from PyPI instead of from the SVN
- add .downloads and .eggs folders
- Raisin web server
- The download paths and the project folders are now configured in the buildout.cfg
- Remove pickle caching code
- Remove code previously used for dumping resources
- Move dumps folder to the top
- improve .gitignore
- pin MySQL-python = 1.2.3
1.7 (2012-07-25)
================
- Fix a bug that prevented the pipeline from building the inclusion exclusion table
- Speed up the recursive mapping part of the pipeline
- The output from the Flux capacitor is not deleted any more, making it available for
further analysis
- When defining accessions, labels written in Python are not supported any more.
- In the Raisin web application, links are now shorter when pointing to pages with tabs.
For example, it is not necessary to add /tab/experiments to URLs any more, if the
experiments tab is the default tab.
1.6 (2012-07-10)
================
- Upgrade to raisin.recipe.server 1.1.3, which now creates the var/log folder needed
when starting raisin with supervisord
- Upgrade to raisin.recipe.load version 1.1.2. Raisin can now be installed even if
some annotation information is missing
- Upgrade to pipeline 6.3 which includes several bug fixes. Now it correctly gets
all the scores in qualities and ambiguous. Parsing reads is fixed, and HiSEq read IDs
are now handled.
1.5 (2012-07-06)
================
- Installs and integrates FastQC
- Default parameters to make configuration easier. When no project
parameters are given, use read_length. When no project user is
given, use anonymous
1.4 (2012-06-27)
================
- Calculate gene and exon RPKM now from the Flux Capacitor results.
- Add script using FastQC, A quality control tool for high throughput sequence data.
- Installs Cufflinks 2.0.1 binaries, and use it to find Novel transcripts
1.3 (2012-05-18)
================
- Different Flux installation procedure, using flux instead of flux.sh
- Upgrade to Flux-Capacitor 1.0 RC2
- Add troubleshooting information for the installation of the Bio::DB::Sam
package
1.2 (2012-04-20)
================
- Install grape.recipe.pipeline from PyPI
- Use hexagonit.recipe.download for installing dependencies
- Improved validation of configurations files
- Add a pointer to the installation instructions to the README.txt
1.1.2 (2012-03-30)
==================
- Moved the installation instructions to INSTALL.txt
- Added README.txt to pipelines/Quick
1.1.1 (2012-03-30)
==================
- Added further setup instructions to the README.txt
1.1 (2012-03-29)
================
- Include a quick run mode, and added pipelines for quickly running Grape
for several species: Homo sapiens, Mus musculus and Drosophila
Melanogaster
1.0 (2012-03-29)
================
- First official release
- Fix package versions to be used in dependencies.cfg
- Adding .eggs and .downloads folder for buildout cache
- readType can now be decoded from shorthands 2x50 and 75D
- cellline parameter for pipeline is now quoted
- mate_id now gets a postfix of .1 and .2
- parameters given on multiple lines are collapsed to a single line
- Upgrade to Pyramid 1.3
- Use grape.recipe.pipeline recipe instead of prepare.py script
- Put dependencies into their own file and point to it from buildout.cfg