Merge pull request #97 from loosolab/estimation_motifs

Estimation motifs

README.md

@@ -6,31 +6,23 @@ For further information read the [documentation](https://github.molgen.mpg.de/lo
 
 ## Dependencies
 * [conda](https://conda.io/docs/user-guide/install/linux.html)
-* [Nextflow](https://www.nextflow.io/)
-* [MEME-Suite](http://meme-suite.org/doc/install.html?man_type=web)
 
 ## Installation
-1. Start with installing all dependencies listed above (Nextflow, conda, MEME-Suite) and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
-2. It is required to set the [environment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).
-this can be done with following commands:
-```
-export PATH=[meme-suite instalation path]/libexec/meme-[meme-suite version]:$PATH
-export PATH=[meme-suite instalation path]/bin:$PATH
-```
+1. Start with installing conda and downloading all files from the [GitHub repository](https://github.molgen.mpg.de/loosolab/masterJLU2018).
 
-3. Every other dependency will be automatically installed using conda. For that a conda environment has to be created from the yaml-file given in this repository.
+2. Every other dependency will be automatically installed using conda. For that a conda environment has to be created from the yaml-file given in this repository.
 It is required to create and activate the environment from the yaml-file beforehand.
 This can be done with following commands:
 ```condsole
 conda env create -f masterenv.yml
 conda activate masterenv
 ```
 
-4. Set the wd parameter in the nextflow.config file as path where the repository is saved. For example: '~/masterJLU2018/'.
+3. Set the wd parameter in the nextflow.config file as path where the repository is saved. For example: '~/masterJLU2018/'.
 
 
 **Important Notes:**
-1. For conda the channel bioconda needs to be set as highest priority! This is required due to two different packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfish package from the channel conda-forge!
+1. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfish package from the channel conda-forge! Please make sure that the right jellyfish package is installed.
 
 
 ## Quick Start
@@ -42,7 +34,7 @@ nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta
 There are files provided inside  ./demo/ for a demo run.
 Go to the main directory and run following command:
 ```
-nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38_chr1.fa --motif_db ./demo/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --organism hg38 --gtf_annotation ./demo\homo_sapiens.94.mainChr.gtf
+nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38_chr1.fa --motif_db ./demo/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --organism hg38 --gtf_annotation ./demo/homo_sapiens.94.mainChr.gtf
 ```
 
 ## Parameters

masterenv.yml

@@ -6,7 +6,7 @@ dependencies:
   - numpy=1.15.4
   - pybigWig
   - cd-hit
-  - jellyfish
+  - bioconda::jellyfish
   - r-base>=3.5.1
   - r-data.table
   - r-pbapply