Conda

CHANGELOG.md

@@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+### `Added`
+-   [#712](https://github.com/SciLifeLab/Sarek/pull/712), [#718](https://github.com/SciLifeLab/Sarek/pull/718) - Added possibilities to run Sarek with `conda`
+
 ### `Changed`
 
 -   [#710](https://github.com/SciLifeLab/Sarek/pull/710) - Improve release checklist and script

README.md

@@ -82,13 +82,14 @@ The Sarek pipeline comes with documentation in the `docs/` directory:
 06. [Configuration and profiles documentation](https://github.com/SciLifeLab/Sarek/blob/master/docs/CONFIG.md)
 07. [Intervals documentation](https://github.com/SciLifeLab/Sarek/blob/master/docs/INTERVALS.md)
 08. [Running the pipeline](https://github.com/SciLifeLab/Sarek/blob/master/docs/USAGE.md)
-09. [Command line parameters](https://github.com/SciLifeLab/Sarek/blob/master/docs/PARAMETERS.md)
-10. [Examples](https://github.com/SciLifeLab/Sarek/blob/master/docs/USE_CASES.md)
-11. [Input files documentation](https://github.com/SciLifeLab/Sarek/blob/master/docs/INPUT.md)
-12. [Processes documentation](https://github.com/SciLifeLab/Sarek/blob/master/docs/PROCESS.md)
-13. [Documentation about containers](https://github.com/SciLifeLab/Sarek/blob/master/docs/CONTAINERS.md)
-14. [More information about ASCAT](https://github.com/SciLifeLab/Sarek/blob/master/docs/ASCAT.md)
-15. [Output documentation structure](https://github.com/SciLifeLab/Sarek/blob/master/docs/OUTPUT.md)
+09. [Running the pipeline using Conda](https://github.com/SciLifeLab/Sarek/blob/master/docs/CONDA.md)
+10. [Command line parameters](https://github.com/SciLifeLab/Sarek/blob/master/docs/PARAMETERS.md)
+11. [Examples](https://github.com/SciLifeLab/Sarek/blob/master/docs/USE_CASES.md)
+12. [Input files documentation](https://github.com/SciLifeLab/Sarek/blob/master/docs/INPUT.md)
+13. [Processes documentation](https://github.com/SciLifeLab/Sarek/blob/master/docs/PROCESS.md)
+14. [Documentation about containers](https://github.com/SciLifeLab/Sarek/blob/master/docs/CONTAINERS.md)
+15. [More information about ASCAT](https://github.com/SciLifeLab/Sarek/blob/master/docs/ASCAT.md)
+16. [Output documentation structure](https://github.com/SciLifeLab/Sarek/blob/master/docs/OUTPUT.md)
 
 ## Contributions & Support
 
@@ -117,6 +118,7 @@ Helpful contributors:
 * [Björn Nystedt](https://github.com/bjornnystedt)
 * [Pall Olason](https://github.com/pallolason)
 * [Aron Skaftason](https://github.com/arontommi)
+* [Nilesh Tawari](https://github.com/nilesh-tawari)
 
 --------------------------------------------------------------------------------
 

conf/conda.config

@@ -0,0 +1,10 @@
+/*
+ * -------------------------------------------------
+ * Nextflow config file for Sarek
+ * -------------------------------------------------
+ * Conda environments for every process
+ * All environment need to be set up
+ * -------------------------------------------------
+ */
+
+process.conda = 'environment.yml'

docs/CONDA.md

@@ -0,0 +1,45 @@
+# Run Sarek using Conda
+
+> /!\\
+This functionality is still under development, so we would recommend to use it with care.
+
+> /!\\
+A conda environment is defined but does not contain all the tools needed for fully using Sarek.
+
+To use Sarek with conda, first make sure that you have conda installed.
+We recommend miniconda:
+https://conda.io/miniconda.html
+
+Sarek comes with a conda environment definition - a file called
+[`environment.yml`](../environment.yml) which lists conda channels and package names/versions.
+
+To run Sarek with Conda, you can use/modify the profile `conda`, or follow the following steps:
+
+1. Create a new environment using the [`environment.yml`](../environment.yml) file:
+
+```bash
+# Download the environment.yml file
+curl https://raw.githubusercontent.com/SciLifeLab/Sarek/master/environment.yml -o environment.yml
+
+# Create a new conda environment using it
+conda env create -f environment.yml
+```
+
+2. Create a nextflow config file as indicated below (Usually as `~/.nextflow/config` file):
+
+```groovy
+process {
+  beforeScript = { 'module load anaconda; set +u; source activate sarek-2.2.2; set -u;' }
+}
+```
+
+3. While launcing Sarek specify the nextflow config file crreated in step 2 using `-c` option:
+
+```bash
+nextflow run SciLifeLab/Sarek/main.nf \
+  --sample samples_germline.tsv \
+  -profile conda \
+  --genome_base /sw/data/uppnex/ToolBox/hg38bundle \
+  --genome GRCh38 \
+  -c ~/.nextflow/config
+```

docs/CONFIG.md

@@ -29,6 +29,12 @@ Define usage limits and Singularity for BINAC cluster in Tuebingen.
 
 Designed for usage with Singularity on CFC at QBic.
 
+### [`conda.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/conda.config)
+
+> /!\\ Under development.
+
+Define conda environement.
+
 ### [`containers.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/containers.config)
 
 Define Containers for all process.
@@ -107,6 +113,13 @@ This is the profile for use on the BTB server munin.
 
 This is the profile for use on the CFC cluster in Tuebingen.
 
+### `conda`
+
+> /!\\ Under development.
+
+This is the profile for conda testing on a small machine, or on Travis CI.
+Conda environement will be built automatically.
+
 ### `docker`
 
 This is the profile for docker testing on a small machine, or on Travis CI.

docs/USAGE.md

@@ -4,7 +4,6 @@ This guide will take you through your first run of Sarek.
 It is divided into two steps corresponding to the two main types of analysis offered by Sarek:
  - Run a Germline Analysis
  - Run a Somatic Analysis
- - Run Sarek using Bioconda
 
 This guide assumes you have internet access on the server where the analysis will take place. If you do not have that, please look into the [installation instructions](INSTALL_BIANCA.md) for the restricted access server Bianca at Uppmax, which should give an idea on how to adjust the following examples accordingly.
 
@@ -183,49 +182,3 @@ nextflow run SciLifeLab/Sarek/runMultiQC.nf \
 -profile slurm
 --project <your uppmax project id> \
 ```
-
-## Run Sarek using Bioconda
-
-To use Sarek with conda, first make sure that you have conda installed. We recommend miniconda:
-https://conda.io/miniconda.html
-
-Sarek comes with a conda environment definition - a file called
-[`environment.yml`](../environment.yml) which lists conda channels and package names/versions. 
-Follow the steps below to run Sarek with Conda:
-
-- Step 1: Create a new environment using the [`environment.yml`](../environment.yml) file:
-
-```bash
-# Download the environment.yml file
-curl https://raw.githubusercontent.com/SciLifeLab/Sarek/master/environment.yml -o environment.yml
-
-# Create a new conda environment using it
-conda env create -f environment.yml
-
-```
-
-- Step 2: Create a nextflow config file as indicated below (Usually as `~/.nextflow/config` file):
-
-```
-process {
-  beforeScript = { 'module load anaconda; set +u; source activate sarek-2.2.2; set -u;' }
-//  errorStrategy = { task.attempt < 2 ? 'retry' : 'finish' }
-// Optionally executor/cluster specific details can be added as indicated below,
-/*   
-  executor='sge'
-  penv='smp'
-*/
-}
-```
-
-- Step 3: While launcing Sarek specify the nextflow config file crreated in step 2 using `-c` option:
-
-```
-nextflow run SciLifeLab/Sarek/main.nf \
---sample samples_germline.tsv \
--profile conda \
---project <your uppmax project id> \
---genome_base /sw/data/uppnex/ToolBox/hg38bundle \
---genome GRCh38
--c ~/.nextflow/config
-```

nextflow.config

@@ -108,8 +108,9 @@ profiles {
   }
   conda {
     includeConfig 'conf/base.config'
+    includeConfig 'conf/travis.config'
     includeConfig 'conf/genomes.config'
-    includeConfig 'conf/resources.config'
+    includeConfig 'conf/conda.config'
   }
 }