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Commit 6a2bd03e authored by Skander Hatira's avatar Skander Hatira
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Testing building packages

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Stage: build
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.gitlab-ci.yml
+ 4
− 1
View file @ 6a2bd03e
......@@ -12,8 +12,11 @@
stages:
- build
before_script:
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
build:
image: jlarky/electron-forge:latest
image: electronjs/build:latest
stage: build
script:
- cd $CI_PROJECT_DIR/
......
Gala_vs_Annaglo-CG.bed deleted 100644 → 0
+ 0
− 12329
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src/backend/helpers/cloneBiseps.js
+ 1
− 1
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......@@ -4,7 +4,7 @@ const cloneBiseps = (body, uniqueDir) => {
const fs = require("fs");
execSync(
`git clone -b slurm git@forgemia.inra.fr:skander.hatira/bissprop.git ${uniqueDir}`,
`git clone git@forgemia.inra.fr:skander.hatira/biseps.git ${uniqueDir}`,
(error, stdout, stderr) => {
if (error) {
console.log(`error: ${error.message}`);
......
src/backend/helpers/createArchive.js
+ 1
− 1
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......@@ -4,7 +4,7 @@ const createArchive = (uniqueDir) => {
const fs = require("fs");
execSync(
`git clone -b slurm git@forgemia.inra.fr:skander.hatira/bissprop.git ${uniqueDir}`,
`git clone git@forgemia.inra.fr:skander.hatira/biseps.git ${uniqueDir}`,
(error, stdout, stderr) => {
if (error) {
console.log(`error: ${error.message}`);
......
src/backend/helpers/createConfig.js
+ 3
− 2
View file @ 6a2bd03e
......@@ -33,11 +33,12 @@ const createConfig = (body, uniqueDir, uniqueDirRemote) => {
: body.genome,
},
adapters: body.remote
? path.join(".test/resources/adapters", body.adapters)
? path.join(".test/resources/adapters", body.adapters, ".fa")
: path.join(
__dirname,
"../../../resources/adapters",
body.adapters
body.adapters,
".fa"
) || "",
},
......
src/backend/helpers/createProfile.js
+ 6
− 2
View file @ 6a2bd03e
......@@ -23,17 +23,21 @@ function createProfile(body, uniqueDir, uniqueDirRemote) {
"default-resources": ["cpus=1", "mem_mb=10000", "time_min=5440"],
"use-conda": true,
"dry-run": body.subsample,
"rerun-incomplete": true,
"latency-wait": 20,
"keep-going": true,
cores: body.cpu || "all",
};
const slurmProfile = {
jobs: body.jobs,
cluster: `sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards} --mail-user=${body.email} `,
jobs: parseInt(body.jobs),
cluster: `"sbatch -t {resources.time_min} --mem={resources.mem_mb} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards} --mail-user=${body.email}"`,
"default-resources": ["cpus=1", "mem_mb=10000", "time_min=5440"],
configfile: body.remote
? "config/config.yaml"
: path.join(uniqueDir, "config/config.yaml"),
"use-conda": true,
"latency-wait": 20,
"rerun-incomplete": true,
"keep-going": true,
"dry-run": body.subsample,
};
......
src/backend/snakemake.js
+ 49
− 4
View file @ 6a2bd03e
......@@ -75,23 +75,68 @@ const spawnChild = async (
if (body.cluster) {
connect(host, function (err, ssh) {
exec(
`cd ${homeDir} && tar -xf workflow.tar.gz && rm -rf ${homeDir}/.snakemake && sbatch slurmScript.sh > slurm.out.txt `,
`cd ${homeDir} && tar -xf workflow.tar.gz && rm -rf .snakemake/ && sbatch exec_scripts/slurmScript.sh `,
{ ssh: ssh },
(err, stdout, stderr) => {
console.log(stdout);
console.log("stdout is:", stdout);
console.log("stderr is:", stderr);
console.log("errors is:", err);
}
);
// exec(
// `cd ${homeDir} && sbatch slurmScript.sh`,
// { ssh: ssh },
// (err, stdout, stderr) => {
// console.log(stdout);
// }
// );
});
// connect(host, function (err, ssh) {
// child = exec(
// {
// command: `cd ${homeDir} && sbatch slurmScript.sh`,
// ssh: ssh,
// },
// function (err, stdout, stderr) {
// console.log(stdout);
// }
// );
// child.stdout.on("data", function (data) {
// console.log(data);
// });
// child.on("exit", function (code) {
// console.log("Exit", code);
// });
// });
} else {
connect(host, function (err, ssh) {
exec(
`cd ${homeDir} && tar -xf workflow.tar.gz && rm -rf ${homeDir}/.snakemake && bash localScript.sh > local.out.txt`,
`cd ${homeDir} && tar -xf workflow.tar.gz && rm -rf .snakemake/ && source exec_scripts/script.sh && bash exec_scripts/localScript.sh`,
{ ssh: ssh },
(err, stdout, stderr) => {
console.log(stdout);
console.log("stdout is:", stdout);
console.log("stderr is:", stderr);
console.log("errors is:", err);
}
);
});
// connect(host, function (err, ssh) {
// child = exec(
// {
// command: `cd ${homeDir} && source localScript.sh`,
// ssh: ssh,
// },
// function (err, stdout, stderr) {
// console.log(stdout);
// }
// );
// child.stdout.on("data", function (data) {
// console.log(data);
// });
// child.on("exit", function (code) {
// console.log("Exit", code);
// });
// });
// const child = execFile(
// localScript,
// [env, profile, workflow],
......
testing.ls.txt
+ 0
− 1
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dist
Gala_vs_Annaglo-CG.bed
hooks.js
node_modules
out
......
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