From 3ae785104fb98aa58a1040c42bf3a2d635ac3e3b Mon Sep 17 00:00:00 2001
From: Skander Hatira <skander.hatira@inrae.fr>
Date: Fri, 1 Oct 2021 13:38:18 +0200
Subject: [PATCH] fix path to openInFolder
---
resources/snakemakeLinux.yaml | 16 ++++++++--------
src/backend/snakemake.js | 12 ++++++------
2 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/resources/snakemakeLinux.yaml b/resources/snakemakeLinux.yaml
index 0bd7078..ce93abb 100644
--- a/resources/snakemakeLinux.yaml
+++ b/resources/snakemakeLinux.yaml
@@ -1,4 +1,4 @@
-name: bisepsSnakemake
+name: snakemakeBiseps
channels:
- bioconda
- defaults
@@ -17,13 +17,13 @@ dependencies:
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- bcrypt=3.2.0=py39h3811e60_1
- - boto3=1.18.50=pyhd8ed1ab_0
- - botocore=1.21.51=pyhd8ed1ab_0
+ - boto3=1.18.51=pyhd8ed1ab_0
+ - botocore=1.21.52=pyhd8ed1ab_0
- 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
- - cachetools=4.2.2=pyhd8ed1ab_0
+ - cachetools=4.2.4=pyhd8ed1ab_0
- cairo=1.16.0=h6cf1ce9_1008
- certifi=2021.5.30=py39hf3d152e_0
- cffi=1.14.6=py39h4bc2ebd_1
@@ -75,7 +75,7 @@ dependencies:
- grpcio=1.38.1=py39hff7568b_0
- gtk2=2.24.33=h539f30e_1
- gts=0.7.6=h64030ff_2
- - harfbuzz=2.9.1=h83ec7ef_0
+ - harfbuzz=2.9.1=h83ec7ef_1
- httplib2=0.19.1=pyhd8ed1ab_0
- icu=68.1=h58526e2_0
- idna=3.2=pyhd3eb1b0_0
@@ -196,8 +196,8 @@ dependencies:
- slacker=0.14.0=py_0
- smart_open=5.2.1=pyhd8ed1ab_0
- smmap=3.0.5=pyh44b312d_0
- - snakemake=6.9.1=hdfd78af_0
- - snakemake-minimal=6.9.1=pyhdfd78af_0
+ - snakemake=6.7.0=hdfd78af_0
+ - snakemake-minimal=6.7.0=pyhdfd78af_0
- sqlite=3.36.0=h9cd32fc_2
- stone=3.2.1=pyhd8ed1ab_0
- stopit=1.1.2=py_0
@@ -234,5 +234,5 @@ dependencies:
- yaml=0.2.5=h516909a_0
- yarl=1.5.1=py39h07f9747_0
- zipp=3.5.0=pyhd8ed1ab_0
- - zlib=1.2.11=h516909a_1010
+ - zlib=1.2.11=h36c2ea0_1011
- zstd=1.5.0=ha95c52a_0
diff --git a/src/backend/snakemake.js b/src/backend/snakemake.js
index af16541..b5b3b0e 100644
--- a/src/backend/snakemake.js
+++ b/src/backend/snakemake.js
@@ -19,6 +19,8 @@ const spawnChild = async (body, profile, uniqueDir, homeDir, unlock) => {
process.platform == "win32" ? "powershell.exe" : process.env.SHELL,
// stdio: ["ignore", output, output],
};
+ const failedArchive = `${uniqueDir}/failed.archive.lock`;
+
if (body.remote) {
const host = {
host: body.machine.hostname,
@@ -34,8 +36,7 @@ const spawnChild = async (body, profile, uniqueDir, homeDir, unlock) => {
!body.rerun
) {
const child = exec(
- `${command} run -n bisepsSnakemake --cwd ${uniqueDir} --no-capture-output --live-stream snakemake --profile ${profile}
- --config platform="other" --archive workflow.tar.gz`,
+ `${command} run -n bisepsSnakemake --cwd ${uniqueDir} --no-capture-output --live-stream snakemake --profile ${profile} --config platform="other" --archive workflow.tar.gz`,
options
);
@@ -56,14 +57,13 @@ const spawnChild = async (body, profile, uniqueDir, homeDir, unlock) => {
});
if (exitCode) {
- const filename = `${uniqueDir}/failed.archive.lock`;
- fs.closeSync(fs.openSync(filename, "w"));
+ fs.closeSync(fs.openSync(failedArchive, "w"));
// throw new Error(`subprocess error exit ${exitCode}, ${error}`);
} else {
const filename = `${uniqueDir}/archive.lock`;
fs.closeSync(fs.openSync(filename, "w"));
- if (fs.existsSync(filename)) {
- fs.unlinkSync(filename);
+ if (fs.existsSync(failedArchive)) {
+ fs.unlinkSync(failedArchive);
}
}
}
--
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