import shutils

README.md

@@ -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)
 
 
 

workflow/tests/test_pool_and_psuedoreplicate.py

@@ -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)