adding git as a dependency of bisepsSnakemake environment .yml

resources/snakemakeLinux.yaml

-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

src/backend/.env

 PORT=5000
 SECRET="secret"
 DATABASE="mongodb://%2Ftmp%2Fbisepsmongodb.sock"
+ACCESS_TOKEN="hFMzsg6x4_dtxF12iqXX"
\ No newline at end of file

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}`);

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}`);