Then, copy `application.properties.example``application.properties`. Configuration will be edited in next step
## Example of installation with Anaconda
## Quick install with conda
All tools except Genomestrip can be installed via anaconda. If you have python3 AND snakemake (which requires python3) in your system, you can install conda only for python2.
All tools except Genomestrip, svtyper and lumpy can be installed via anaconda or miniconda.
Here, we choose to install all softwares with python3 conda, except lumpy and svtyper which still requires python2. We will use miniconda to just install what we need.
We test the install with python3 miniconda.
### 1. Install miniconda
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@@ -73,62 +73,41 @@ Here, we choose to install all softwares with python3 conda, except lumpy and sv
Then, follow the steps.
### 2. Load conda environment
### 2. Load base conda environment
export PATH=$CONDA_HOME/bin:$PATH
export PERL5LIB="$CONDA_HOME/lib/perl5:$PERL5LIB"
Where `$CONDA_HOME` is the folder in which you install miniconda in previous step.
### 3. Install snakemake
Where `$CONDA_HOME` is the folder in which you install miniconda in previous step.
If we use conda to do it (with default conda config), we have an older version (3.13.3). So we can just use pip to do it to have the latest version (4.7.0):
### 3. Create the conda environment
pip install snakemake==4.7.*
conda create --name cnv --file requirements.txt
This will install snakemake into the conda environment (loaded in previous step)
### 4. Install softwares in the default environment
Note: if some softwares are already present in the system (or as modules), you don't need to install them in conda (except if their version is not compatible with the pipeline)
conda install -c bioconda delly==0.7.7
conda install -c bioconda pindel==0.2.5b9
conda install -c bioconda samtools==1.7
conda install -c bioconda bedtools==2.26.0
conda install -c r r
conda install -c bioconda exonerate==2.4.0
conda install -c bioconda picard==2.17.11
### 4. Load new conda environment
Then, install all modules listed above with `pip` command.
source activate cnv
export PERL5LIB="$CONDA_HOME/envs/cnv/lib/perl5"
### 5. Create python2 environment inconda
Where `$CONDA_HOME` is the folder in which you install miniconda in previous step.
### 6. Install softwares in the python2 environment
You must then install [genomestrip](http://software.broadinstitute.org/software/genomestrip/) and [lumpy](https://github.com/arq5x/lumpy-sv) using their install procedure.
conda install -c bioconda lumpy-sv==0.2.13
conda install -c bioconda svtyper==0.1.4
conda install -c bioconda repeatmasker==4.0.6
conda install -c bioconda vcftools==0.1.11
conda install -c bioconda parallel
Note: the latest versions of vcftools - 0.1.15 - does not contains vcf-sort in conda (it's not the case outside of conda...). So in conda, we install the 0.1.11 version.
You also need to install the RepBase (http://www.girinst.org/server/archive/RepBase21.12/ - choose this version as more recent ones are not compatible with 4.0.6 version of RepeatMaster), then define the path to the Library folder inside the application.properties file (see below).
Note: RepeatMasker is installed inside the python2 environment as it's not compatible with delly because of incompatible requirements.
Special case of genologin cluster (genotoul):
Note: you need to install then the RepBase (http://www.girinst.org/server/archive/RepBase21.12/ - choose this version as more recent ones are not compatible with 4.0.6 version of RepeatMaster), then define the path to the Library folder inside the application.properties file (see below).
### For future logins
* Lumpy is already available through bioinfo/lumpy-v0.2.13. Just add it in the application.properties file.
* For genomestrip, you can use this folder: `/usr/local/bioinfo/src/GenomeSTRiP/svtoolkit_2.00.1774` (see configuration part, sv_dir point)
### 6. Future logins
For future logins, you must reactivate all conda environments. This means launching these commands:
