From 383b3c1f2663c7959b3d56dcd2fb37d8230698d0 Mon Sep 17 00:00:00 2001
From: Helene Rimbert <helene.rimbert@inra.fr>
Date: Fri, 12 Jan 2024 14:02:47 +0100
Subject: [PATCH] DOCS: remove absolut path from doc and examples
---
docs/source/install.md | 2 +-
docs/source/pipeline_conf.md | 2 +-
docs/source/run_pipeline.md | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/docs/source/install.md b/docs/source/install.md
index 90a8095..bfb67f6 100644
--- a/docs/source/install.md
+++ b/docs/source/install.md
@@ -12,7 +12,7 @@ $ git clone https://forgemia.inra.fr/umr-gdec/magatt.git
We recommend to build the environment using conda (developped with miniconda 3, conda 4.9.2 ) with the file [environment.yml](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/envs/environment.yml):
```console
-$ conda env create -f environment.yml -n magatt
+$ conda env create -f envs/environment.yml -n magatt
```
Once created, you can activate the environment with:
diff --git a/docs/source/pipeline_conf.md b/docs/source/pipeline_conf.md
index e5feeb0..ed5423a 100644
--- a/docs/source/pipeline_conf.md
+++ b/docs/source/pipeline_conf.md
@@ -31,7 +31,7 @@ Here, we only need the fasta of the new genome assembly
| Parameter in `config.yaml` | format |description |Example |
|----------------------------|--------|------------|--------|
|**targetFasta**|FASTA|fasta file of the target genome assembly on which we transfert the annotation|targetFasta: 'data/CS_pesudo_v2.1.fa'|
-|**targetBwaIdx**|BWA index|Prefix for the BWA index files|targetBwaIdx: '/data/db/triticum_aestivum/arinalrfor/current/bwa/all'|
+|**targetBwaIdx**|BWA index|Prefix for the BWA index files|targetBwaIdx: '/data/db/triticum_aestivum/julius/current/bwa/all'|
|**targetGmapIndex**|PATH|Name of the GMAP index directory. This will be used with the `-d` option of `gmapl`|targetGmapIndex: 'ensembl_Triticum_aestivum_julius_2022-9-16'|
|**targetGmapIndexPath**|PATH|Full path to the directory in which the GMAPindex is found. This will be used with the `-D` option of `gmapl`|targetGmapIndexPath: '/data/db/triticum_aestivum/julius/gmapdb/all/'|
diff --git a/docs/source/run_pipeline.md b/docs/source/run_pipeline.md
index 5e54a68..f355363 100644
--- a/docs/source/run_pipeline.md
+++ b/docs/source/run_pipeline.md
@@ -32,7 +32,7 @@ $ snakemake -j 32 --cluster sbatch
This will allow to have at most 32 subproccess run through the SLURM scheduler with `sbatch`.
-You can use a custom [cluster.json](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/cluster.json) JSON file do setup the parameters of SBATCH for each rules, and use it with with:
+You can use a custom [cluster.json](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/cluster-hpc2.json) JSON file do setup the parameters of SBATCH for each rules, and use it with with:
```console
$ snakemake -j 32 --cluster-config cluster-hpc2.json --cluster "sbatch -J {cluster.jobName} -c {cluster.c} --mem {cluster.mem} -e {cluster.error} -o {cluster.output} -p gdec" --verbose"
--
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