https://github.com/likelet/workflow
https://github.com/likelet/workflow
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/likelet/workflow
- Owner: likelet
- Created: 2017-04-15T05:55:42.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2017-05-12T02:40:59.000Z (about 8 years ago)
- Last Synced: 2025-01-07T20:45:54.718Z (4 months ago)
- Size: 4.88 KB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Workflow
## 1. Description
A collection of self-developed bioinformatics analysis pipeline coding by a DSL language, nextflow.
To run the pipeline files with nf suffixed, plz just type the following command.
```
nextflow -c nextflow.config -with-trace
```
If the pipeline fails at any point and you fix the issue, you can revoke the processes with job avoidance using this command:
```
nextflow -c nextflow.config -with-trace -resume
```
All those pipelines were written in Nextflow commands. For more details, please see the following link:
https://www.nextflow.io/
## 2. Installation of dependencies.
### Install NextFlow
To run our pipelines. NextFlow should be preinstalled at POSIX compatible system (Linux, Solaris, OS X, etc), It requires BASH and Java 7 or higher to be installed. We do not recommend running the pipes in the Windows since most of bioinformatic tools do not supported.
Here, we show the step by step installation of NextFlow in linux system as an example, which adapted from [NextFlow](https://www.nextflow.io/docs/latest/getstarted.html).
1. Download the executable package by copying and pasting the following command in your terminal window: ```wget -qO- get.nextflow.io | bash```. It will create the nextflow main executable file in the current directory.
2. Optionally, move the nextflow file in a directory accessible by your `$PATH` variable (this is only required to avoid to remember and type the Nextflow full path each time you need to run it).
3. Download the lastest binary verion of NextFlow from the https://github.com/nextflow-io/nextflow/releases and add the path into your system environment.
### Install third-party software and database required by each pipe.
#### Pipe 1
##### introduction
##### References, index and annotation files（required）
1. STAR index (hg38 genome index etc.)
2. Genome reference (genome fasta file with suffix .fa , UCSC etc).
3. GENCODE gene annotation file in GTF format:
[gencode.v26.annotation.gtf](ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz)
4. LNCipedia gene annotation file in GTF format:
[lncipedia_4_0_hc_hg38.gtf](http://www.lncipedia.org/downloads/lncipedia_4_0_hc_hg38.gtf)
##### software and tools (required)
1. [STAR](https://github.com/alexdobin/STAR), Reference https://www.ncbi.nlm.nih.gov/pubmed/23104886
2. [Cufflinks](https://github.com/cole-trapnell-lab/cufflinks), Reference https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146043/
3. [Bedops](http://bedops.readthedocs.io/en/latest/), Reference https://www.ncbi.nlm.nih.gov/pubmed/22576172/
4. [PLEK](www.ibiomedical.net), Reference
```Shell
wget https://sourceforge.net/projects/plek/files/PLEK.1.2.tar.gz/download
tar -zvxf PLEK.1.2.tar.gz
cd PLEK.1.2
python PLEK_setup.py
```
5. [CNCI](https://github.com/www-bioinfo-org/CNCI), Renference
``` Shell
git clone [email protected]:www-bioinfo-org/CNCI.git
cd CNCI
unzip libsvm-3.0.zip
cd libsvm-3.0
make
cd ..
```
6. [CPAT](http://rna-cpat.sourceforge.net), Reference
```Shell
wget https://sourceforge.net/projects/rna-cpat/files/?source=navbar
tar zxf CPAT-VERSION.tar.gz
cd CPAT-VERSION
python setup.py install
python setup.py install --root=/home/user/CPAT
export PYTHONPATH=/home/user/CPAT/usr/local/lib/python2.7/site-packages:$PYTHONPATH.
export PATH=/home/user/CPAT/usr/local/bin:$PATH #setup PATH
```