Commit 53ea1c71 authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

import shutils

parent f47e96ee
Pipeline #4375 failed with stages
in 6 seconds
......@@ -133,22 +133,22 @@ If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know
Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
## Programs and Versions
+ python/3.6.1-2-anaconda [website](https://www.anaconda.com/download/#linux) [citation](docs/references.txt)
+ trimgalore/0.4.1 [website](https://github.com/FelixKrueger/TrimGalore) [citation](docs/references.txt)
+ cutadapt/1.9.1 [website](https://cutadapt.readthedocs.io/en/stable/index.html) [citation](docs/references.txt)
+ bwa/intel/0.7.12 [website](http://bio-bwa.sourceforge.net/) [citation](docs/references.txt)
+ samtools/1.6 [website](http://samtools.sourceforge.net/) [citation](docs/references.txt)
+ sambamba/0.6.6 [website](http://lomereiter.github.io/sambamba/) [citation](docs/references.txt)
+ bedtools/2.26.0 [website](https://bedtools.readthedocs.io/en/latest/) [citation](docs/references.txt)
+ deeptools/2.5.0.1 [website](https://deeptools.readthedocs.io/en/develop/) [citation](docs/references.txt)
+ phantompeakqualtools/1.2 [website](https://github.com/kundajelab/phantompeakqualtools) [citation](docs/references.txt)
+ macs/2.1.0-20151222 [website](http://liulab.dfci.harvard.edu/MACS/) [citation](docs/references.txt)
+ UCSC_userApps/v317 [website](https://genome.ucsc.edu/util.html) [citation](docs/references.txt)
+ R/3.4.1 [website](https://www.r-project.org/) [citation](docs/references.txt)
+ python/3.6.1-2-anaconda [website](https://www.anaconda.com/download/#linux) [citation](docs/references.md)
+ trimgalore/0.4.1 [website](https://github.com/FelixKrueger/TrimGalore) [citation](docs/references.md)
+ cutadapt/1.9.1 [website](https://cutadapt.readthedocs.io/en/stable/index.html) [citation](docs/references.md)
+ bwa/intel/0.7.12 [website](http://bio-bwa.sourceforge.net/) [citation](docs/references.md)
+ samtools/1.6 [website](http://samtools.sourceforge.net/) [citation](docs/references.md)
+ sambamba/0.6.6 [website](http://lomereiter.github.io/sambamba/) [citation](docs/references.md)
+ bedtools/2.26.0 [website](https://bedtools.readthedocs.io/en/latest/) [citation](docs/references.md)
+ deeptools/2.5.0.1 [website](https://deeptools.readthedocs.io/en/develop/) [citation](docs/references.md)
+ phantompeakqualtools/1.2 [website](https://github.com/kundajelab/phantompeakqualtools) [citation](docs/references.md)
+ macs/2.1.0-20151222 [website](http://liulab.dfci.harvard.edu/MACS/) [citation](docs/references.md)
+ UCSC_userApps/v317 [website](https://genome.ucsc.edu/util.html) [citation](docs/references.md)
+ R/3.4.1 [website](https://www.r-project.org/) [citation](docs/references.md)
+ SPP/1.14
+ meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](docs/references.txt)
+ ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](docs/references.txt)
+ DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](docs/references.txt)
+ meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](docs/references.md)
+ ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](docs/references.md)
+ DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](docs/references.md)
......
......@@ -5,6 +5,7 @@ import pandas as pd
from io import StringIO
import os
import pool_and_psuedoreplicate
import shutil
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/design/'
......@@ -63,8 +64,7 @@ def test_check_controls_single(design_experiment_3):
@pytest.mark.unit
def test_single_rep(design_experiment_2):
cwd = os.getcwd()
B_1 = open(cwd + '/B_1.bedse.gz', "w+")
B_1.close()
shutil.copy('/work/BICF/s189701/chipseq_analysis/test_data/B_1.bedse.gz', cwd)
single_rep = pool_and_psuedoreplicate.generate_design('false', 1.2, design_experiment_2, cwd, 1, 1)
......
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