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Octocat-spinner-32 R.methodsS3 adding R libraries
Octocat-spinner-32 R.oo adding R libraries
Octocat-spinner-32 cmdline Added dependency checking, .gitignore
Octocat-spinner-32 dependencies Changes to print dependencies, Changes to email when complete
Octocat-spinner-32 example Update msg.cfg
Octocat-spinner-32 instructions Changes to print dependencies, Changes to email when complete
Octocat-spinner-32 tests Ignore changes in non-deterministic output files when testing.
Octocat-spinner-32 tools Updated benchmarking tool, updated simulator, added prototype paramet…
Octocat-spinner-32 .gitignore updated ignore file for testing
Octocat-spinner-32 README Changes to print dependencies, Changes to email when complete
Octocat-spinner-32 TQSfastq.py Changes for new mapping algorithms
Octocat-spinner-32 Utils.pm Improved python dependency output and runs it earlier
Octocat-spinner-32 barcode_splitter.py Made compressed files compatible with illumina index parsing
Octocat-spinner-32 breakpoint-widths.R First commit
Octocat-spinner-32 countalleles.c First commit
Octocat-spinner-32 create_stats.py Pre-unzip reads file for new parser. Update how parsing stats are cre…
Octocat-spinner-32 ded.R First commit
Octocat-spinner-32 extract-ref-alleles.py Improved memory handling
Octocat-spinner-32 fastq_2_fasta.pl adding fastq_2_fasta file
Octocat-spinner-32 filter-sam.py Brought over Tina hu's changes to be compatible with later versions o…
Octocat-spinner-32 fit-hmm.R Added back in rec rate handling
Octocat-spinner-32 grepfqparser.py Pre-unzip reads file for new parser. Update how parsing stats are cre…
Octocat-spinner-32 hmmlib.R revert accidental commit
Octocat-spinner-32 hmmprob_to_est.py Added another row to file format, added memory and time tracking
Octocat-spinner-32 hmmprobs.c revert accidental commit
Octocat-spinner-32 make-pileups.sh Changed pileup to us -B option
Octocat-spinner-32 makefile First commit
Octocat-spinner-32 mapping_functions.py Don't overwrite stats file on reruns
Octocat-spinner-32 msg.pl Added back in rec rate handling
Octocat-spinner-32 msgCluster.pl Added back in rec rate handling
Octocat-spinner-32 msgUpdateParentals.pl Added new custom qsub option in config files to be used in ALL qsub c…
Octocat-spinner-32 msglib.py Changed extract ref alleles to dynamically determine how much system …
Octocat-spinner-32 parent1or2-hmm.sh Added back in rec rate handling
Octocat-spinner-32 parse_BCdata2BWA.pl Added new parsing option, updated validation of parents in update par…
Octocat-spinner-32 parse_and_map.py Pre-unzip reads file for new parser. Update how parsing stats are cre…
Octocat-spinner-32 plot_error.R only plot if there exists at least one data point
Octocat-spinner-32 print_dependencies.sh more dependency printing
Octocat-spinner-32 reformatFasta4sam.pl Finished changes to accept gzipped input (but backed out changes to c…
Octocat-spinner-32 send_email.py Changes to print dependencies, Changes to email when complete
Octocat-spinner-32 summaryPlots.R fixed chrom printing
Octocat-spinner-32 summary_mismatch.pl Fixed issue where newlines were being included in barcode names when …
Octocat-spinner-32 test_dependencies.sh Test dependencies before running MSG
Octocat-spinner-32 test_dependencies_R.R Added dependency checking, .gitignore
Octocat-spinner-32 test_dependencies_R.sh Added dependency checking, .gitignore
Octocat-spinner-32 test_dependencies_executable.sh Fixed how dep. script checks Python version, updated README to point …
Octocat-spinner-32 test_dependencies_perl.pl Test dependencies before running MSG
Octocat-spinner-32 test_dependencies_python.py Added dependency checking, .gitignore
Octocat-spinner-32 updateRef.pl first attempt at making trimming and updating updating parents steps …
Octocat-spinner-32 validate.py Fixed validation so it can handle underscores in barcodes and tsv files
Octocat-spinner-32 version updated version
Octocat-spinner-32 write-hmm-data.R Changes for new mapping algorithms
README
MSG: Multiplexed Shotgun Genotyping
http://genomics.princeton.edu/AndolfattoLab/MSG.html
https://github.com/JaneliaSciComp/msg
http://www.ncbi.nlm.nih.gov/pubmed/21233398

### Dependencies ###
Run test_dependencies.sh to check for the existence of dependencies

NOTE: Most of these packages can be found in the dependencies directory for you to 
extract and install as needed on your system.

Python (2.6.4)
bwa (0.5.7)
samtools (0.1.9-3)  ! Newer versions of Samtools will not work !
biopython-1.53
Pyrex-0.9.9
pysam-0.1.2 (apply fix as described here: http://code.google.com/p/pysam/issues/detail?id=22&can=1&q=dandavison0)
R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 1.2.0 and R.oo 1.7.3)
Perl Modules (IO::Uncompress::Gunzip)
    -- A command like this should work on Unix Desktop Systems:
    -- perl -MCPAN -e 'install IO::Uncompress::Gunzip'
mailer (Python package: http://pypi.python.org/pypi/mailer) - optional; for sending email alert when run completes

### Installation instructions ###
git clone git://github.com/JaneliaSciComp/msg.git
cd msg
make

### Toy Example ###
The toy example is useful to check that MSG and dependencies are installed and functioning correctly.
TODO

### Example with Real Data ###
Download the data from NCBI's Sequence Read Archive and MSG config and barcodes file
 - example/get_sample_data.sh (requires wget)

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