Bowtie Code

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Myrna: Cloud-scale differential expression for RNA-seq
http://bowtie-bio.sf.net/myrna

Myrna NEWS
==========

   Myrna is now available for download.  1.0.0-beta2 was the first
version to be released, and it was released under the OSI Artistic
License (see LICENSE file) and freely available to the public for
download.  The current version is 1.2.1.

Reporting Issues
================

Please report any issues using the Sourceforge bug tracker:

  https://sourceforge.net/tracker/?group_id=236897&atid=1101606

Version Release History
=======================

Version 1.2.1 - August 9, 2012
   * Fixed issue where some Perl versions would cause pipeline to crash
     in Normalize step.
   * Fixed issue whereby spurious characters could be added to label
     names, causing a crash in the Normalize step.

Version 1.2.0 - July 19, 2012
   * Added support for Hadoop version 0.20.205.
   * Dropped support for Hadoop versions prior to 0.20.
   * Updated default Hadoop version for EMR jobs to 0.20.205.
   * Updated Bowtie version used to 0.12.8.
   * Updated R version used to 2.14.2.
   * Updated jar files to use Ensembl v67 (used to be v61).  In the
     process, fixed an issue whereby $MYRNA_HOME/reftools scripts
     would die due to unexpected new format of Ensembl database schema.
   * Fixed issues with streaming jar version parsing
   * Fixed documentation bugs regarding --sra-toolkit option, which is
     superseded by the --fastq-dump option.
   * Removed some diagnostic counters because Hadoop began to enforce
     an upper limit on the number of counters allowed per job.  For
     instance, per-label summary statistics are no longer printed in
     the Normalize step.

Version 1.1.2 - May 23, 2011
   * Updated jar files to use Ensembl v61 (used to be v58).
   * Added --from-middle option that causes a read's overlap
     "influence" to be measured from the middle of the read rather than
     from one of the ends.
   * Added --just-align and --resume-align options.  --just-align
     causes Myrna to put the results of the Alignment phase in the
     --output directory and quit after the alignment phase.  You can
     later "resume" Myrna by specifying this directory as the --input
     directory and specifying the --resume-align option.
   * Fixed issue with .sra input whereby status output from fastq-dump
     would be interpreted as a read.
   * Other minor bugfixes.

Version 1.1.1 - February 7, 2011
   * Added support for the .sra file format, used by the Sequence Read
     Archive.  These files can now be specified in the manifest.  Myrna
     uses the fastq-convert tool from the SRA Toolkit to convert .sra
     files to .fastq files in the preprocess stage.
   * The examples that included defunct SRA FASTQ files were updated to
     point to new .sra files instead.
   * Fixed labeling scheme in $MYRNA_HOME/example/human/full.manifest
     to use proper <Group ID>-<BioRep ID>-<TechRep ID> format.
   * Removed the --union-constitutive gene footprint which was
     effectively superseded by the --union-intersection footprint.
   * Fixed issues with the Ensembl.pl/Ensembl.R scripts that would
     cause them to abort when no exons were marked as constitutive.
   * Upgraded Bowtie version to 0.12.7.

Version 1.0.9 - September 13, 2010
   * Fixed bug in cloud mode that would cause crashing in the Map
     portion of the Postprocess stage
   * Fixed example manifests that point to Short Read Archive files to
     use .bz2 instead of .gz extensions.

Version 1.0.8 - September 4, 2010
   * Set the memory cap on the sort task to be inversely proportional
     to --cpus, to avoid memory footprint blowup on computers with more
     processors.
   * Fixed a final issue that affected how Myrna handles quality
     value conversion.
   * Fixed issue whereby bzip2'ed data would be handled incorrectly by
     the preprocessor.
   * Fixed counter in Preprocess step that would erroneously refer to
     unpaired reads as paired.  Also "Read data fetched to EC2" has
     been changed to "Read data fetched".
   * In EMR mode, updated where user credentials are found; Amazon
     changed their path sometime around 8/30/2010.
   * In EMR mode, updated the manner in which the bootstrap action is
     specified; the old way was disabled by Amazon sometime around
     8/30/2010.
   * Fixed issue whereby ReduceWrap.pl would crash in cases with a
     large number of bins (>10 million) .
   * NOTE: The Short Read Archive (SRA) seems to be in the midst of a
     reorganization that includes files that were previously gzipped
     being replaced with versions zipped with bzip2.  The files will
     sometimes disappear for a while.  If you are having problems with
     an example where input reads come from the SRA, try renaming files
     in the manifest file as appropriate.  If that doesn't work, please
     contact us.

Version 1.0.7 - August 27, 2010
   * Fixed issue whereby the order of the arguments to bowtie would
     result in a crash when POSIXLY_CORRECT is set.
   * Fixed --keep-all option, which was causing a crash.
   * Fixed a lingering quality bug whereby qualities were converted
     immediately to phred33 but phred64 or solexa64 flags would be
     spuriously passed to Bowtie.

Version 1.0.6 - August 26, 2010
   * Single-computer mode now copies the output that it writes to the
     console to a file 'myrna.local.(pid).out'.  Please include the
     contents of this file when reporting issues.
   * Sorting in single-computer mode is now more portable; switched
     from command-line sort to pure-Perl File::Sort.
   * Fixed issue with mkdir commands that failed under some OSs.
   * More helpful output from MapWrap.pl and ReduceWrap.pl to make it
     easier to debug issues in single-computer-mode runs.
   * Fixed issue where web form would incorrectly convert + signs in
     AWS secret key to spaces, causing some good credentials to fail
     verification.
   * Fixed issue in preprocessor that mishandles copies when user's AWS
     secret key contains slash characters.

Version 1.0.5 - August 16, 2010
   * Fixed issue that prevented MYRNA_EMR_HOME environment variable
     from working.
   * Fixed issue whereby Align.pl script fails to report a count for
     the number of reads with alignments sampled due to Bowtie's -M
     option.
   * Fixed issue that made it difficult to specify a space-separated
     list of arguments to the --bowtie-args and other --*-args
     parameters.
   * Fixed issue whereby most documentation referred to arguments with
     a single-dash prefix, whereas users with the POSIXLY_CORRECT
     environment variable set must use a double-dash prefix.
     Documentation and code have been updated to always use double-dash
     prefixes.

Version 1.0.4 - July 22, 2010
   * A web-based GUI for composing and submitting Myrna Elastic
     MapReduce jobs has been added.  Most helpfully, the web GUI has
     features for sanity-checking inputs; e.g. whether the user's
     credentials as entered are valid, whether the input URL exists,
     etc.
   * Updated EMR and Hadoop modes to support Hadoop 0.20.  0.20 is now
     the default mode for myrna_emr (and for the elastic-mapreduce
     script)
   * When starting a cloud-mode job from the command line, the
     elastic-mapreduce script must be at least as new as Amazon's
     2010-06-02 release
   * Many improvements to the manual, including fixes to the examples
     and pointers to Amazon's new AWS Console tool for interacting with
     S3
   * Various bugfixes

Version 1.0.0-beta6 - July 12, 2010
   * Fixed several documentation issues.
   * Updated pre-built jars and scripts to use Ensembl 58.
   * Added RPKM calculation.
   * Added output files encoding the calculated normalization factors.

Version 1.0.0-beta2 - May 17, 2010
   * Beta release of Myrna, a tool for investigating differential gene
     expression in very large RNA-seq datasets.