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Readme.md

GEM-Tools

GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.

The C API currently supports fast and exhaustive support for parsing GEM .map files and other mapping formats.

The Python gem module allows to integrate the GEM Mapper in python scripts and simplifies development of mapping pipelines.

In addition to the library functionality, GEM-Tools also provides a command line tool gemtools, that you can use to start the RNASeq pipeline and various other tools, like the indexer and the statistics module.

Licensing

The Python modules also distributes current GEM binaries that are compatible with the library code. Note that the GEM binaries are distributed under the GEM Non commercial binary license while the GEM-Tools is licensed under GPL.

Contact

If you have any questions or you run into problems, feel free to join the gemtools mailing list at gemtools@googlegroups.com

Installation

The GEM-Tools library is distributed in three different flavors. You can get a statically compiled binary bundle if you are just interested in teh command line tools. If you would like to explore the library functionality, you can install the latest release from pypi. If you want to get the latest and greatest, you can clone the git repository and install the library from source.

Static distribution

The GEM-Tools command line tools are bundled and distributed as a static binary bundle that includes all dependencies. You do not have to install any other software to use the binary bundle, but you will not be able to write your own python scripts. You are restricted to the available command line tools.

NOTE that the GEM binaries are compiled with optimizations for i3 processors. We also provide a bundle for older CPU's that lack certain features. If you are not sure which package to download, i3 or core2, run the following command on the machine you want to install GEM-Tools:

python -c 'print ("i3 compatible" if set(["popcnt", "ssse3", "sse4_1", "sse4_2"]).issubset(set([f for sl in map(lambda x:x.split(), filter(lambda x:x.startswith("flags"), open("/proc/cpuinfo").readlines())) for f in sl])) else "No i3 support detected. Please use the core2 bundle")'

This command checks your /proc/cpuinfo file for the flags popcnt, ssse3, sse4_1 and sse4_2 are present. If that is the case, the CPU is supported by the i3 bundle. Otherwise use core2.

The latest release can be downloaded here:

Library distribution

In order to install the GEM-Tool library on your system and get access to the command line tools as well as the library functionality, you need to have a couple of dependencies installed. Unfortunately we can currently not install those dependencies for you. After all dependencies are installed, you have all the options to build and install the library in your local machine. These include:

  • Install a released version from pypi
  • Install form the git repository
  • Build the library bundle
  • Build the static binary distribution

Dependencies

The C API needs to have gzlib and bzlib installed with header files. Both libraries are used to transparently open compressed files. On a Debian/Ubuntu system the packages are libbz2-dev and zlib-dev.

Here is an example of how you can install the necessary dependencies to build the C-library on a Debian/Ubuntu system:

sudo apt-get install make gcc libbz2-dev

For the python part, the library will work both with Python 2.6 and Python 2.7. In order to compile the the C binding, you need to have Cython installed, as well as the python header files.

Here is an example of how you can install the necessary dependencies to build the Python library on a Debian/Ubuntu system:

sudo apt-get install make gcc libbz2-dev python-dev

Install from pypi

Gemtools is distributed through pypi and you can install the latest released version using pip or easy_install. But please make sure you have all the dependencies installed first.

As root:

pip install gemtools

As non-root user:

pip install gemtools --user

Install from github

You can install GEM-Tool from the github repository using the distributed setup.py script.

Clone the repository

git clone https://github.com/gemtools/gemtool

Change into the gemtools folder and install the python library

cd gemtools

As root:

python setup.py install

As non-root user:

python setup.py install --user 

This will install into a $HOME/.local folder and you might want to add $HOME/.local/bin to your path. For example, add

export PATH=$PATH:$HOME/.local/bin

to your ~/.bashrc to make the change permanent.

Build the library package

From the repository, you can build the python library package. This you can use to moved to a dedicated folder and can be managed by your prefered module manager easily.

In order to build the library package, clone the the repository and call

make package

This will create a dist/ folder that contains two tarballs, one for i3, and one for core2. In addition you will see the unpacked folders. They are structured as follows:

bin/ -- all the executables
lib/ -- symlink to lib64
lib64/ -- contains the gemtools c library as limgemtools.a
lib64/python<version>/site-packages -- the python libraries for your python version (i.e. 2.6 or 2.7)
include/ -- the C API header files

Say you moved the package to /opt/gemtools and you run python2.6. You can activate the package by exporting the following variables to your environment:

export PATH=$PATH:/opt/gemtools/bin
export PYTHONPATH=$PYTHONPATH:/opt/gemtools/lib64/python2.6/site-packages

This will make all the executables available in your path and put the python library into the python search path so you can leverage it from your scripts.

Build the static binary bundle

If you are not interested in using any python library functions from your script, you can build portable static binary package by calling the dist target in the Makefile.

make dist

This will create a dist/ folder that contains two tarballs, one for i3, and one for core2. In addition you will see the unpacked folders. They are structured as follows:

bin/ -- all the executables
lib/ -- symlink to lib64
lib64/ -- contains the gemtools c library as limgemtools.a
include/ -- the C API header files

Say you moved the package to /opt/gemtools. You can activate the package by exporting the following variables to your environment:

export PATH=$PATH:/opt/gemtools/bin

Bugs and feature requests

Please feel free to use the Github bug tracker to report issues and feature requests that you find in the GEM-Tools library.

If you run into problems with GEM and the included GEM binaries, please use the GEM bugtracker.

Change log

1.7.1
- Fixed issue with fasta files where no qualities are provided
- Fixed issue with cutom output folder in the RNA-Pipeline and where
  the transcriptome was not put into the desired location
- Fixed issue with single end reads in the id cleanup step in the 
  rna-pipeline
- Added coverage calculation to gtfstats run in the rna-pipeline. The
  coverage stats will be contained in the .json file.

1.7
- Fixed issue with junctions of length 0 in gtf extraction
- Added filtered output to default rna-pipeline output
- An exception is thrown when the initial splitmap file contains a 
  "!" in the strata field
- Add ability to replace a single executable and use the bundled 
  ones for the rest
- Add fail-checks when passing input to functions that expect a ReadIterator
- Refactor the RNASeq pipeline construction into a standalone class
- The statically compiled gemtools is now compatible with kernel 2.6.18
- Fixedgt.filter memory leak
- Set XT:U based on uniqueness level, i.e. 1:0:0:1 is level 2
- Chimeric reads in GEM and SAM
- Include a function to reconstruct the read after a trimmed alignment
- Add a annotation mapping filter to the pipeline to reduce multi-maps
- Implement a parallel merger for files with different size 
  (subset of reads)
- Add distance resort to gt.filter to support rnaseq mappings where 
  splits should not be counted as an event
- Fixed gt.filter output FASTQ pairdend reads
- Add a split-map only filter to the pipeline/transcriptome mapping step
- Add --keep-unique option to the gt.filter to disable filtering 
  for all mappings with exactly one alignment
- Speedup for merge operations for reads with lots of mappings
- Add JSON support to gt.stats
- Add json support to gt.gtfcounts
- Add coverage counts to gt.gtfcount

1.6.2
- Fixed issue with compute-transcriptome
- Fixed issue with gem-2-sam where XS flag could not be computed
- Added additional flag to avoid XS computation

1.6.1
- GEMTools SAM conversion doesnow include the header again
- Pair detection fixed for reads with space in the id and not casava
- Pipeline -o paramter does create the output folder now automatically
- samtools sorter max memory is now properly set for the non-threads version
- Added option to create sam-compact format in the pipeline

1.6
- Parallel file conversion for pipeline
- Cython C bindings for the parser library
- JSON export of the statistics
- Index and transcript index support from gemtools
- Restartable pipeline options
- gem-2-sam now writes the XS field for cufflinks support
- Added the new rna seq pipeline
- Added stats and report tools to the gemtools cli tool
- Added new bundle system and detection for i3 vs core2
- Added optional appending NH field to SAM entries
- Added *extra* options to mapper/splitmapper/pairalign to enable 
  passing custom command line options to the tools.
- Modify C::counters_functions to use zero-based indexes

1.5
- Fixed issues with gem-rna-mapper output and validation
- Moved validation to be a default step after split-mapping
- Added stats filter
- Fixed issue with gem-2-sam binary
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