diff --git a/resources/snakemakeLinux.yaml b/resources/snakemakeLinux.yaml index ce93abbb39161b365e6459e4074a69b1cdee1192..afe14d9d223743deeb69e84ca8c468e8b12f258a 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 e4b517ba946ab40b5de8de7aed0a642ae750f47a..13ae382df30bdfe4f26d41fd5424e74aa342b5ed 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 19bac9312f169c2e233556d02e50a8f0dc10a1e8..fb91b2893ab7a0eef17b5b37a907e40d1db484ba 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 ed61dc0dd8c7d66e5d875b2539f8fb0667001dd2..d94b476c9b10b7543b8929642908004db169d615 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}`);