Update README.md

README.md

@@ -10,20 +10,27 @@ For further information read the [documentation](https://github.molgen.mpg.de/lo
 * [MEME-Suite](http://meme-suite.org/doc/install.html?man_type=web)
 
 ## Installation
-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).
-It is required to set the [enviroment paths for meme-suite](http://meme-suite.org/doc/install.html?man_type=web#installingtar).
+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 [enviroment 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
 ```
 
-Every other dependency will be automatically  installed by Nextflow using conda. For that a new conda enviroment will be created, which can be found in the from Nextflow created work directory after the first pipeline run.
-It is **not** required to create and activate the enviroment from the yaml-file beforehand.
+3. Every other dependency will be automatically  installed using conda. For that a conda enviroment has to be created from the yaml-file given in this repository.
+It is required to create and activate the enviroment from the yaml-file beforehand.
+This can be done with following commands:
+```condsole
+conda env create -f masterenv.yml
+conda activate masterenv
+```
+
 
 **Important Note:** 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!
 
 
+
 ## Quick Start
 ```console
 nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]
@@ -39,52 +46,44 @@ Required arguments:
 	--config		 Path to UROPA configuration file
  	--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
 	--out			 Output Directory (Default: './out/')
-
 Optional arguments:
-
 	--help [0|1]		1 to show this help message. (Default: 0)
 	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.
 	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
 				 Path can be set as tfbs_path in next run. (Default: './')
 	--gtf_path			Path to gtf-file. If path is set the process which creats a gtf-file is skipped.
-
 	Footprint extraction:
 	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)
 	--step INT		This parameter sets the number of positions to slide the window forward. (Default: 100)
 	--percentage INT	Threshold in percent (Default: 0)
-
 	Filter unknown motifs:
 	--min_size_fp INT	Minimum sequence length threshold. Smaller sequences are discarded. (Default: 10)
 	--max_size_fp INT	Maximum sequence length threshold. Discards all sequences longer than this value. (Default: 100)
-
+	--tfbsscan_method [moods|fimo] Method used by tfbsscan. (Default: moods)
 	Clustering:
 	Sequence preparation/ reduction:
 	--kmer INT		Kmer length (Default: 10)
 	--aprox_motif_len INT	Motif length (Default: 10)
 	--motif_occurence FLOAT	Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif.
 	--min_seq_length Interations	Remove all sequences below this value. (Default: 10)
-
 	Clustering:
 	--global INT		Global (=1) or local (=0) alignment. (Default: 0)
 	--identity FLOAT	Identity threshold. (Default: 0.8)
 	--sequence_coverage INT	Minimum aligned nucleotides on both sequences. (Default: 8)
 	--memory INT		Memory limit in MB. 0 for unlimited. (Default: 800)
 	--throw_away_seq INT	Remove all sequences equal or below this length before clustering. (Default: 9)
 	--strand INT		Align +/+ & +/- (= 1). Or align only +/+ (= 0). (Default: 0)
-
 	Motif estimation:
 	--min_seq INT 		Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100)
 	--motif_min_key INT	Minimum number of key positions (aligned columns) in the alignment done by GLAM2. (Default: 8)
 	--motif_max_key INT	Maximum number of key positions (aligned columns) in the alignment done by GLAM2.f (Default: 20)
 	--iteration INT		Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000)
 	--tomtom_treshold float	Threshold for similarity score. (Default: 0.01)
 	--best_motif INT	Get the best X motifs per cluster. (Default: 3)
-
 	Moitf clustering:
 	--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0)
 	--edge_weight INT	Minimum weight of edges in motif-cluster-graph (Default: 5)
 	--motif_similarity_thresh FLOAT	Threshold for motif similarity score (Default: 0.00001)
-
 	Creating GTF:
 	--tissues List/String 	List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON
 				config
@@ -94,20 +93,6 @@ All arguments can be set in the configuration files
 For further information read the [documentation](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki).
 
 ## Known issues
-The Nextflow-script needs a conda environment to run. Nextflow creates the needed environment from the given yaml-file.
-On some systems Nextflow exits the run with following error:
-```
-Caused by:
-  Failed to create Conda environment
-  command: conda env create --prefix  --file env.yml
-  status : 143
-  message:
-```
-If this error occurs you have to create the environment before starting the pipeline.
-To create this environment you need the yml-file from the repository.
-Run the following commands to create the environment:
-```console
-path=[Path to given masterenv.yml file]
-conda env create --name masterenv -f $path
-```
-When the environment is created, set the variable 'path_env' in the configuration file as the path to it.
+
+For unknown reasons Moods, whisch is called by tfbsscan, rarely returns empty bedfiles. If this happens The pipeline stops.
+The is no known fix sofar. If it happens try starting the pipeline again. If it still fails. Change the parameter tfbsscan_method to 'fimo'. This methods takes longer but will cause no error.