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Commit 9ae8673d authored by christine.tranchant_ird.fr's avatar christine.tranchant_ird.fr
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Completing installation description

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......@@ -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
......
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