From 9ae8673dc6b554130afda26b0bbe357435147c12 Mon Sep 17 00:00:00 2001
From: christine <christine.tranchant@ird.fr>
Date: Fri, 12 Jan 2024 17:24:13 +0100
Subject: [PATCH] Completing installation description
---
README.rst | 132 ++++++++++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 120 insertions(+), 12 deletions(-)
diff --git a/README.rst b/README.rst
index acc346d..e60558d 100644
--- a/README.rst
+++ b/README.rst
@@ -24,6 +24,7 @@ Requirement
Clone the git repository
-----------------
+* Caution, still in development mode... but installation will be more straightforward soon.
::
@@ -33,15 +34,8 @@ Clone the git repository
cd PATH_2_FRANGIPANE_DIRECTORY
python3 -m pip install -U pip setuptools build
- python3 -m pip install -e .
-
-
-.. code-block:: rst
-
- NOTE : Updating snakecdysis package (ref) using by frangiPANe if necessary
-
- python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
-
+ python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
+ python3 -m pip install .
1.2 Install frangiPANe tool
@@ -53,6 +47,8 @@ Choose only one mode
* in a cluster mode
::
+ module load <SINGULARITY_NAME>
+ module load <PYTHON_VERSION>
frangiPANe install_cluster -s slurm -e singularity
@@ -75,17 +71,94 @@ Download or build the singularity container in the container directory
::
+ cd path2frangipane_directory/frangiPANe/frangiPANe/containers/
+
# Download the container
wget https://itrop.ird.fr/frangiPANe/frangiPANe.sif
- # OR build the container
- singularity build frangiPANe.sif frangiPANe.def
+
Checking if frangiPANe has been correctly installed
-----------------
+* Run the `frangiPANe` command, the following lines have to print if all i alright :
+
+::
+
+
+
+
+
+ ad88 88 88888888ba db 888b 88
+ d8' '' 88 "8b d88b 8888b 88
+ 88 88 ,8P d8'`8b 88 `8b 88
+ MM88MMM 8b,dPPYba, ,adPPYYba, 8b,dPPYba, ,adPPYb,d8 88 88aaaaaa8P' d8' `8b 88 `8b 88 ,adPPYba,
+ 88 88P' "Y8 '' `Y8 88P' `"8a a8" `Y88 88 88''''''' d8YaaaaY8b 88 `8b 88 a8P_____88
+ 88 88 ,adPPPPP88 88 88 8b 88 88 88 d8''''''''8b 88 `8b 88 8PP''''''
+ 88 88 88, ,88 88 88 "8a, ,d88 88 88 d8' `8b 88 `8888 '8b, ,aa
+ 88 88 `'8bbdP'Y8 88 88 `'YbbdP'Y8 88 88 d8' `8b 88 `888 `'Ybbd8''
+ aa, ,88
+ 'Y8bbdP'
+
+ A modular and interactive application to simplify the construction of a panreference using the map-then-assembly approach."
+
+ Version Version 1.0
+
+ @author: Sebastien Ravel and Christine Tranchant
+ @email: christine.tranchant@ird.fr
+
+ Please cite our github: https://forge.ird.fr/diade/frangipane
+
+ Licencied under CeCill-C (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html)
+ and GPLv3 Intellectual property belongs to IRD, CIRAD and authors.
+
+ Documentation avail at: https://frangiPANe.readthedocs.io/en/latest/
+
+
+ ** NOTE: This frangiPANe version (Version 1.0) is higher than the production version (There aren’t any releases), you are using a dev version
+
+
+ Usage: frangiPANe [OPTIONS] COMMAND [ARGS]...
+
+ Options:
+ -r, --restore Restore previous installation to use again "install_local" or "install_cluster" [default: False]
+ -e, --install_env print Install path, Tools config, Install mode, Tools install mode, Current version, Latest version avail, Snakecdysis version
+ [default: False]
+ -v, --version Show the version and exit.
+ -h, --help Show this message and exit.
+
+ Commands:
+ create_config Create config.yaml for run
+ edit_cluster_config Edit cluster_config.yaml use by profile
+ edit_tools Edit own tools version
+ run_cluster Run workflow on HPC
+ show_tools show tools version
+ test_install Test frangiPANe cluster mode with "data_test"
+
+
+* Run the command `frangiPANe edit_tools` to check the path of the container and modify the name of modules to load if necessary (cluster mode):
+
::
- frangiPANe
+ 1 ## BUILD SINGULARITY IMAGES PATH
+ 2 ## PLEASE FILL IN SINGULARITY IMAGES PATH IF YOU HAVE CHOSEN INSTALL WITH ENV MODE SINGULARITY (option --env singularity)
+ 3 ## PLEASE FILL IN "ENVMODULES" SECTION IF YOU HAVE CHOSEN INSTALL WITH ENV MODE MODULES (option --env modules)
+ 4 ## WARNING!!! DO NOT ERASE LINES OR COMMENT THEM ! è_é
+ 5
+ 6 SINGULARITY:
+ 7
+ 8 TOOLS : '/scratch/tranchant/frangipane/frangiPANe/containers/frangiPANe.sif'
+ 9
+ 10 # Is and exemple of tools path
+ 11 ENVMODULE:
+ 12 ABYSS : "abyss"
+ 13 BWA : "bwa"
+ 14 EA-UTILS : "ea-utils"
+ 15 SAMTOOLS : "samtools"
+ 16 ASSEMBLY-STATS : "assembly-stats"
+ 17 CD-HIT : "cdhit"
+ 18 FASTQ_STATS: "fastq_stats"
+ 19 FASTQ_STATS: "fastq_stats"
+ 20 NCBI-TOOLS: "ncbi-tools++"
**FrangiPANe structure**
@@ -147,11 +220,46 @@ III - Run FrangiPANe
**cluster mode**
+* Configure slurm jobs with the command `frangiPANe edit_cluster_config`
+
::
+
+ 1 __default__:
+ 2 cpus-per-task: 1
+ 3 mem-per-cpu: 6G
+ 4 partition: normal
+ 5 nodelist: node1
+ 6 output: '{log.output}_cluster'
+ 7 error: '{log.error}_cluster'
+ 8 job-name: '{rule}.{wildcards}'
+ 9
+ 10 abyss:
+ 11 cpus-per-task: 3
+ 12
+ 13 bwa_mem:
+ 14 cpus-per-task: 4
+ 15
+ 16 samtools_view:
+ 17 cpus-per-task: 3
+ 18
+ 19 samtools_flagstat:
+ 20 cpus-per-task: 3
+ 21
+ 22 #vecscreen
+ 23
+ 24 #create_panref
+
+* Launch your first analysis with frangiPANe. Start with data-test !
+
+::
+
module load python/3.8.12
frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml --cluster-config /scratch/tranchant/frangipane/frangiPANe/install_files/cluster_config_ITROP.yaml
+
+> example of bash script
+
::
#!/bin/bash
--
GitLab