From 6a97468324998292a97b707ca69b648878f1049e Mon Sep 17 00:00:00 2001
From: Skander Hatira <skander.hatira@inrae.fr>
Date: Fri, 18 Feb 2022 10:57:41 +0100
Subject: [PATCH] adding git as a dependency of bisepsSnakemake environment
.yml
---
resources/snakemakeLinux.yaml | 12 +++++++-----
src/backend/.env | 1 +
src/backend/helpers/cloneBiseps.js | 2 +-
src/backend/helpers/createArchive.js | 2 +-
4 files changed, 10 insertions(+), 7 deletions(-)
diff --git a/resources/snakemakeLinux.yaml b/resources/snakemakeLinux.yaml
index ce93abb..afe14d9 100644
--- a/resources/snakemakeLinux.yaml
+++ b/resources/snakemakeLinux.yaml
@@ -1,8 +1,9 @@
-name: snakemakeBiseps
+name: bisepsSnakemake
channels:
- bioconda
- - defaults
+ - anaconda
- conda-forge
+ - defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
@@ -22,10 +23,10 @@ dependencies:
- brotlipy=0.7.0=py39h3811e60_1001
- bzip2=1.0.8=h7f98852_4
- c-ares=1.17.2=h7f98852_0
- - ca-certificates=2021.5.30=ha878542_0
+ - ca-certificates=2020.10.14=0
- cachetools=4.2.4=pyhd8ed1ab_0
- cairo=1.16.0=h6cf1ce9_1008
- - certifi=2021.5.30=py39hf3d152e_0
+ - certifi=2021.10.8=py39h06a4308_2
- cffi=1.14.6=py39h4bc2ebd_1
- chardet=4.0.0=py39hf3d152e_1
- charset-normalizer=2.0.0=pyhd8ed1ab_0
@@ -59,6 +60,7 @@ dependencies:
- gettext=0.21.0=hf68c758_0
- ghostscript=9.54.0=h9c3ff4c_1
- giflib=5.2.1=h516909a_2
+ - git=2.23.0=pl526hacde149_0
- gitdb=4.0.7=pyhd8ed1ab_0
- gitpython=3.1.24=pyhd8ed1ab_0
- google-api-core=1.31.2=pyhd8ed1ab_0
@@ -142,7 +144,7 @@ dependencies:
- oauth2client=4.1.3=py_0
- olefile=0.46=pyh9f0ad1d_1
- openjpeg=2.4.0=hb52868f_1
- - openssl=1.1.1l=h7f98852_0
+ - openssl=1.1.1m=h7f8727e_0
- packaging=21.0=pyhd8ed1ab_0
- pandas=1.3.3=py39hde0f152_0
- pango=1.48.10=hb8ff022_1
diff --git a/src/backend/.env b/src/backend/.env
index e4b517b..13ae382 100644
--- a/src/backend/.env
+++ b/src/backend/.env
@@ -1,3 +1,4 @@
PORT=5000
SECRET="secret"
DATABASE="mongodb://%2Ftmp%2Fbisepsmongodb.sock"
+ACCESS_TOKEN="hFMzsg6x4_dtxF12iqXX"
\ No newline at end of file
diff --git a/src/backend/helpers/cloneBiseps.js b/src/backend/helpers/cloneBiseps.js
index 19bac93..fb91b28 100644
--- a/src/backend/helpers/cloneBiseps.js
+++ b/src/backend/helpers/cloneBiseps.js
@@ -4,7 +4,7 @@ const cloneBiseps = (body, uniqueDir) => {
const fs = require("fs");
execSync(
- `git clone https://forgemia.inra.fr/skander.hatira/biseps.git ${uniqueDir}`,
+ `git clone https://o2auth:${process.env.ACCESS_TOKEN}@forgemia.inra.fr/skander.hatira/biseps.git ${uniqueDir}`,
(error, stdout, stderr) => {
if (error) {
console.log(`error: ${error.message}`);
diff --git a/src/backend/helpers/createArchive.js b/src/backend/helpers/createArchive.js
index ed61dc0..d94b476 100644
--- a/src/backend/helpers/createArchive.js
+++ b/src/backend/helpers/createArchive.js
@@ -4,7 +4,7 @@ const createArchive = (uniqueDir) => {
const fs = require("fs");
execSync(
- `git clone git@forgemia.inra.fr:skander.hatira/biseps.git ${uniqueDir}`,
+ `git clone https://o2auth:${process.env.ACCESS_TOKEN}forgemia.inra.fr/skander.hatira/biseps.git ${uniqueDir}`,
(error, stdout, stderr) => {
if (error) {
console.log(`error: ${error.message}`);
--
GitLab