#This pipeline provide the port for running RNA ref and RNA denovo pipeline chenjunhui/RNAport is licensed under the
GNU General Public License v3.0 Permissions of this strong copyleft license are conditioned on making available complete source code of licensed works and modifications, which include larger works using a licensed work, under the same license. Copyright and license notices must be preserved. Contributors provide an express grant of patent rights.
The port is used for preparing config file for RNA reference and RNA denovo. The Click package was used for command port.Three subcommands getdata, rnadenovo and rnarefcfg was included in the main software.
This RNAport was tested by python 3.6 under Linux wh-login-13-1.wh.hpc system. The software depends on click and xlrd packages.
You can install it by pip or raw code just as the following command.
git clone https://github.com/chenjunhui/RNAport
cd RNAport && python3.6 setup.py install --user --prefix=$PREFIX_PATH ($PREFIX_PATH should be included PYTHONPATH, if not, you should export PYHTONPATH="$PREFIX_PATH/lib/python3.6/site-packages")
export PYHTONPATH="$PREFIX_PATH/lib/python3.6/site-packages"
pip install --install-option="--prefix=$PREFIX_PATH" RNAport==1.0
The port contain 3 subcommands: getdata, rnadenvo and rnarefcfg. if you install it successfully. Then you can run it as following
export PATH="$PREFIX_PATH/bin:$PATH"
RNAport --help
Usage: RNAport [OPTIONS] COMMAND [ARGS]...
Welcome to use the RNAKit for preparing config of RNA pipeline. :param
verbosity: :param version: :return: Contact: [email protected]
Options:
-v, --verbosity [info|debug] Verbosity level, default=info.
--version Print version number
-h, --help Show this message and exit.
Commands:
getdata get raw data list for RNA reference pipeline
rnadenvo
rnarefcfg ...
- sub command getdata
RNAport getdata --help
Usage: RNAport getdata [OPTIONS]
get raw data list for RNA reference pipeline
Options:
--rawdir TEXT path of raw data
--bmsinfo TEXT BMS information, format: code sample library
--outfile TEXT output file
-h, --help Show this message and exit.
- sub command rnadenvo
RNAport rnadenvo --help
Usage: RNAport rnadenvo [OPTIONS] DENOVOCONFIG
Options:
--rawdir TEXT path of raw data
--bmsinfo TEXT BMS information, format: code sample library
--outfile TEXT output file
--rename rename sample name in the project
--diffmethod TEXT Gene Diff Expression method
--managermail TEXT project manager email
--analysismail TEXT Analysis email
--subcode TEXT subcode of the project
--projectname TEXT Project name
--speciename TEXT specie Name
--group TEXT group of analysis
--queue TEXT queue of analysis
--cleandata INTEGER data size of clean data
--platform TEXT sequencing Platform
-h, --help Show this message and exit.
- sub command rnarefcfg
RNAport rnarefcfg --help
Usage: RNAport rnarefcfg [OPTIONS] REFCONFIG
indexFiles=['refMrna.fa','chrALL.fa.dict','chrALL.fa.1.ht2l','refMrna.gtf'
,'refPep.fa','specie.nr.desc','gene2tr.txt'] :param RNArefcfg: :param
projectFile: :param rename: :param diffMethod: :param indexdir: :param
managerMail: :param analysisMail: :param subCode: :param projectName:
:param specieName: :param group: :param queue: :param CleanData: :param
platForm: :return:
Options:
--rawdir TEXT path of raw data
--bmsinfo TEXT BMS information, format: code sample library
--outfile TEXT output file
--projectfile TEXT project file provided
--rename rename sample name in the project
--diffmethod TEXT Gene Diff Expression method
--indexdir TEXT directory of genome database index
--managermail TEXT project manager email
--analysismail TEXT Analysis email
--subcode TEXT subcode of the project
--projectname TEXT Project name
--speciename TEXT specie Name
--group TEXT group of analysis
--queue TEXT queue of analysis
--cleandata INTEGER data size of clean data
--platform TEXT sequencing Platform
-h, --help Show this message and exit.
chenjhbio [email protected] or [email protected]
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