c3g · shaloo · Sep 24, 2024 · Sep 24, 2024
diff --git a/docs/source/common/gp_cluster_ini.inc b/docs/source/common/gp_cluster_ini.inc
@@ -1,5 +1,5 @@
 .. tip::
 
-     Depending upon the cluster where you are executing the pipeline, substitute the ``beluga.ini`` file name in the command with the appropriate *clustername.ini* file located in the ``$MUGQIC_PIPELINES_HOME/pipelines/common_ini`` folder.  
+     Depending upon the cluster where you are executing the pipeline, substitute the ``beluga.ini`` file name in the command with the appropriate *clustername.ini* file located in the ``$GENPIPES_INIS/common_ini`` folder.  
 
      For e.g., ``narval.ini``, ``cedar.ini``, or ``graham.ini``.
diff --git a/docs/source/deploy/access_gp_pre_installed.rst b/docs/source/deploy/access_gp_pre_installed.rst
@@ -114,7 +114,6 @@ To load the GenPipes modules, paste the following lines of code and save the fil
    ## GenPipes/MUGQIC genomes and modules
    export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
    module use $MUGQIC_INSTALL_HOME/modulefiles
-   module load mugqic/python/3.11.1
    module load mugqic/genpipes/<latest_version>
    export JOB_MAIL=<my.name@my.email.ca>
    export RAP_ID=<my-rap-id>
@@ -161,7 +160,6 @@ For MUGQIC analysts, add the following lines to your $HOME/.bash_profile:
   fi
 
   module use $MUGQIC_INSTALL_HOME/modulefiles $MUGQIC_INSTALL_HOME_DEV/modulefiles
-  module load mugqic/python/3.11.1
   module load mugqic/genpipes/<latest_version>
 
   export RAP_ID=<my-rap-id>

diff --git a/docs/source/deploy/dep_gp_cloud_gcp.rst b/docs/source/deploy/dep_gp_cloud_gcp.rst
@@ -127,8 +127,8 @@ Step 4: Create ChIP Sequencing pipeline execution command script as shown below:
 
   bash # You do not need this line if you did a logout login cycle
   # The next line generates the pipeline script
-  genpipes chipseq -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.base.ini \
-  $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.cedar.ini \
+  genpipes chipseq -c $GENPIPES_INIS/chipseq/chipseq.base.ini \
+  $GNEPIPES_INIS/common_ini/chipseq.cedar.ini \
   quick_start.ini \
   -j slurm \
   -r readsets.chipseqTest.chr22.tsv \

diff --git a/docs/source/deploy/dep_gp_local.rst b/docs/source/deploy/dep_gp_local.rst
@@ -16,22 +16,25 @@ For more details on other available options to deploy and access GenPipes you ma
 
 .. _docs_download_gp_src:
 
-Step 1: Download latest GenPipes sources
+Step 1: Download latest GenPipes sources and install with pip
 ----------------------------------------
 First of all, visit GenPipes `Download Page <https://bitbucket.org/mugqic/genpipes/downloads/>`_ and get a copy of the latest stable release software.  To fetch the most recent version of GenPipes, you may use the following command:
 
 ::
 
   git clone git@bitbucket.org:mugqic/genpipes.git
+  cd <bitbucket_repo>
+  pip install .
 
 Step 2: Setup environment variables
 -----------------------------------
 
-Add the following line in your your *$HOME/.bash_profile*: to set MUGQIC_PIPELINES_HOME to your local copy path. For example,
+Add the following lines in your your *$HOME/.bash_profile*: to set MUGQIC_PIPELINES_HOME to your local copy path. For example,
 
 ::
 
   export MUGQIC_PIPELINES_HOME=/path/to/your/local/genpipes
+  export GENPIPES_INIS=$MUGQIC_PIPELINES_HOME/genpipes/pipelines
 
 .. _accessing_sw_mod_genomes_local_dp:
 
@@ -267,7 +270,7 @@ You are now all set to use GenPipes pipelines. For each pipeline, you can get he
 
 ::
 
-  genpipes $MUGQIC_PIPELINES_HOME/pipelines/<pipeline_name>/<pipeline_name> --help
+  genpipes <pipeline_name> --help
 
 Running pipelines requires other inputs such as :ref:`Configuration File<docs_config_ini_file>`, :ref:`Readset File<docs_readset_file>` and :ref:`Design File<docs_design_file>`. For details on how to run individual pipelines you can see :ref:`Running GenPipes<docs_using_gp>` or :ref:`GenPipes User Guide<docs_user_guide>`.
 

diff --git a/docs/source/faq/faq_gp_dev.rst b/docs/source/faq/faq_gp_dev.rst
@@ -54,7 +54,7 @@ Now save the updated custom.ini file and mention it on the command line after th
 
 .. code::
 
-      genpipes chipseq -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini custom.ini -r readset.chipseq.txt -d design.chipseq.txt -s 1-20 -g chipseqScript.sh
+      genpipes chipseq -c $GENPIPES_INIS/chipseq/chipseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini custom.ini -r readset.chipseq.txt -d design.chipseq.txt -s 1-20 -g chipseqScript.sh
 
       bash chipseqScript.sh
 

diff --git a/docs/source/get-started/concepts/config_ini_file.rst b/docs/source/get-started/concepts/config_ini_file.rst
@@ -52,20 +52,20 @@ Each pipeline has several configuration files in:
 ::
 
     #!bash
-    $MUGQIC_PIPELINES_HOME/pipelines/<pipeline_name>/<pipeline_name>.*.ini
+    $GENPIPES_INIS/<pipeline_name>/<pipeline_name>.*.ini
 
 A default configuration file (``.base.ini`` extension) is set for running on abacus cluster using Homo sapiens reference genome and must always be passed first to the ``--config`` option.
 
 You can also add a list of other configuration files to ``--config``. Files are read in the list order and each parameter value is overwritten if redefined in the next file.
 
-This is useful to customize settings for a specific cluster or genome. Each pipeline has a special configuration file for beluga and cedar clusters (``.beluga.ini`` and ``.cedar.ini`` extensions respectively) in the same directory. And various genome settings are available in ``$MUGQIC_PIPELINES_HOME/resources/genomes/config/``.
+This is useful to customize settings for a specific cluster or genome. Each pipeline has a special configuration file for beluga and cedar clusters (``.beluga.ini`` and ``.cedar.ini`` extensions respectively) in the same directory. And various genome settings are available in ``$MUGQIC_INSTALL_HOME/genomes/species/``.
 
 For example, to run the DNA-Seq pipeline on beluga cluster with Mus musculus reference genome:
 
 ::
 
     #!bash
-    genpipes $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq --config $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini $MUGQIC_PIPELINES_HOME/resources/genomes/config/Mus_musculus.GRCm38.ini [other options] -g genpipes_command_list.sh
+    genpipes $GENPIPES_INIS/dnaseq/dnaseq --config $GENPIPES_INIS/dnaseq/dnaseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini $MUGQIC_INSTALL_HOME/genomes/species/Mus_musculus.GRCm38//Mus_musculus.GRCm38.ini [other options] -g genpipes_command_list.sh
     bash genpipes_command_list.sh
 
 
diff --git a/docs/source/get-started/concepts/readset_file.rst b/docs/source/get-started/concepts/readset_file.rst
@@ -219,17 +219,17 @@ Readsets refer to replicates that belong to a particular sample. If a sample was
 Creating a Readset File
 =======================
 
-If you have access to Abacus, we provide a script ``$MUGQIC_PIPELINES_HOME/utils/nanuq2mugqic_pipelines.py`` that can access your Nanuq data, creates symlinks to the data on Abacus and creates the Readset file for you.
+If you have access to Abacus, we provide a script ``nanuq2mugqic_pipelines.py`` that can access your Nanuq data, creates symlinks to the data on Abacus and creates the Readset file for you.
 
-If your data is on nanuq but you do not have access to Abacus, there is a helper script ``$MUGQIC_PIPELINES_HOME/utils/csvToreadset.R`` that takes a csv file downloadable from nanuq and creates the Readset file. However, you will have to download the data from Nanuq yourself.
+If your data is on nanuq but you do not have access to Abacus, there is a helper script ``csvToreadset.R`` that takes a csv file downloadable from nanuq and creates the Readset file. However, you will have to download the data from Nanuq yourself.
 
-If your data is not on nanuq, you will have to manually create the Readset file. You can use a template and enter your samples manually. Remember that it is a tab separated file. There is a helper ``$MUGQIC_PIPELINES_HOME/utils/mugqicValidator.py`` script that can validate the integrity of your readset file.
+If your data is not on nanuq, you will have to manually create the Readset file. You can use a template and enter your samples manually. Remember that it is a tab separated file. There is a helper ``mugqicValidator.py`` script that can validate the integrity of your readset file.
 
 .. note::
 
      **For abacus users with Nanuq readsets**
 
-     If your readsets belong to a `Nanuq <http://gqinnovationcenter.com/services/nanuq.aspx>`_ project, use ``$MUGQIC_PIPELINES_HOME/utils/nanuq2mugqic_pipelines.py`` script to automatically create a Readset File and symlinks to your readsets on abacus.
+     If your readsets belong to a `Nanuq <http://gqinnovationcenter.com/services/nanuq.aspx>`_ project, use ``nanuq2mugqic_pipelines.py`` script to automatically create a Readset File and symlinks to your readsets on abacus.
 
 .. Add a note from Francois via Paul S regarding Sample definition
 

diff --git a/docs/source/get-started/using_gp.rst b/docs/source/get-started/using_gp.rst
@@ -93,9 +93,9 @@ Please ensure you have access to the "beluga" server in `Digital Research Allian
 
 ::
 
-  genpipes chipseq -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.chipseq.txt -s 1-15 -g chipseq_cmd.sh
+  genpipes chipseq -c $GENPIPES_INIS/chipseq/chipseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.chipseq.txt -s 1-15 -g chipseq_cmd.sh
 
-To understand what $MUGQIC_PIPELINES_HOME refers to, please see instructions on how to :ref:`access GenPipes on Compute Canada servers<docs_access_gp_pre_installed>`.
+To understand what $GENPIPES_INIS refers to, please see instructions on how to :ref:`access GenPipes on Compute Canada servers<docs_access_gp_pre_installed>`.
 
 In the command above, 
 
@@ -109,7 +109,7 @@ By default, Slurm scheduler is used when using the GenPipes deployment on the `D
 
 ::
 
-  genpipes chipseq -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chiseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/abacus.ini -r readset.chipseq.txt -s 1-15 -j pbs -g chipseq_cmd.sh
+  genpipes chipseq -c $GENPIPES_INIS/chipseq/chiseq.base.ini $GENPIPES_INIS/common_ini/abacus.ini -r readset.chipseq.txt -s 1-15 -j pbs -g chipseq_cmd.sh
 
 The above command generates a list of instructions that need to be executed to run the ChIP sequencing pipeline. These instructions are stored in the file:
 
@@ -208,7 +208,7 @@ Let us now run this RNA-Sequencing analysis on the *beluga* server at `Digital R
 
 ::
 
-  genpipes rnaseq -c $MUGQIC_PIPELINES_HOME/pipelines/rnaseq/rnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -g rnaseqScript.txt
+  genpipes rnaseq -c $GENPIPES_INIS/rnaseq/rnaseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -g rnaseqScript.txt
   bash rnaseqScript.txt
 
 The commands will be sent to the job queue and you will be notified once each step is done. If everything runs smoothly, you should get **MUGQICexitStatus:0** or **Exit_status=0.** If that is not the case, then an error has occurred after which the pipeline usually aborts. To examine the errors, check the content of the **job_output** folder.

diff --git a/docs/source/resources/testCommands.txt b/docs/source/resources/testCommands.txt
@@ -1,39 +1,39 @@
 ::
 
-    genpipes ampliconseq -c $MUGQIC_PIPELINES_HOME/pipelines/ampliconseq/ampliconseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.ampliconseq.txt -s 1-8 -g ampliconseqCommands.sh
+    genpipes ampliconseq -c $GENPIPES_INIS/ampliconseq/ampliconseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.ampliconseq.txt -s 1-8 -g ampliconseqCommands.sh
 
 :: 
 
-    genpipes chipseq -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readsets.chipseq.txt -d design.chipseq.txt -s 1-19 -g chipseqCommands.sh
+    genpipes chipseq -c $GENPIPES_INIS/chipseq/chipseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readsets.chipseq.txt -d design.chipseq.txt -s 1-19 -g chipseqCommands.sh
 
 
 :: 
 
-    genpipes rnaseq -c $MUGQIC_PIPELINES_HOME/pipelines/rnaseq/rnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -s 1-21 -g rnaseqCommands.sh
+    genpipes rnaseq -c $GENPIPES_INIS/rnaseq/rnaseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -s 1-21 -g rnaseqCommands.sh
 
 
 ::
 
-    genpipes dnaseq -t germline_snv -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.dnaseq.txt -s 1-27 -g dnaseqCommands_mugqic.sh
+    genpipes dnaseq -t germline_snv -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.dnaseq.txt -s 1-27 -g dnaseqCommands_mugqic.sh
 
-    genpipes dnaseq -t germline_sv -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.sv.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.dnaseq.txt -s 1-25 -g dnaseq_svCommands.sh
+    genpipes dnaseq -t germline_sv -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini $GENPIPES_INIS/dnaseq/dnaseq.sv.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.dnaseq.txt -s 1-25 -g dnaseq_svCommands.sh
 
-    genpipes dnaseq -t germline_high_cov -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.high_cov.ini  $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.dnaseq.txt -s 1-15 -g dnaseq_high_coverageCommands.sh
+    genpipes dnaseq -t germline_high_cov -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini $GENPIPES_INIS/dnaseq/dnaseq.high_cov.ini  $GENPIPES_INIS/common_ini/beluga.ini -r readset.dnaseq.txt -s 1-15 -g dnaseq_high_coverageCommands.sh
 
-    genpipes dnaseq -t somatic_ensemble -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.cancer.ini  $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.somatic_ensemble.txt -s 1-38 -g dnaseq_somatic_ensembleCommands.sh
+    genpipes dnaseq -t somatic_ensemble -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini $GENPIPES_INIS/dnaseq/dnaseq.cancer.ini  $GENPIPES_INIS/common_ini/beluga.ini -r readset.somatic_ensemble.txt -s 1-38 -g dnaseq_somatic_ensembleCommands.sh
 
 
 ::
 
-    genpipes rnaseq_light -c $MUGQIC_PIPELINES_HOME/pipelines/rnaseq_light/rnaseq_light.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -s 1-8 -g rnaseqLightCommands.sh
+    genpipes rnaseq_light -c $GENPIPES_INIS/rnaseq_light/rnaseq_light.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -s 1-8 -g rnaseqLightCommands.sh
 
 
-    genpipes rnaseq_denovo_assembly -c $MUGQIC_PIPELINES_HOME/pipelines/rnaseq_denovo_assembly/rnaseq_denovo_assembly.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -s 1-24 -g rnaseqDeNovoCommands.sh
+    genpipes rnaseq_denovo_assembly -c $GENPIPES_INIS/rnaseq_denovo_assembly/rnaseq_denovo_assembly.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt -s 1-24 -g rnaseqDeNovoCommands.sh
 
 
 :: 
 
-    genpipes methylseq -c $MUGQIC_PIPELINES_HOME/pipelines/methylseq/methylseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/common_ini/beluga.ini -r readset.methylseq.txt -s 1-15,17-18 > methylseq.sh
+    genpipes methylseq -c $GENPIPES_INIS/methylseq/methylseq.base.ini $GENPIPES_INIS/common_ini/beluga.ini -r readset.methylseq.txt -s 1-15,17-18 > methylseq.sh
 
 
 .. include:: /common/gp_cluster_ini.inc