From 558f56117f2d8bb1039ef5103b65200e134b23f3 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 15:33:06 +0100
Subject: [PATCH 01/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 39af8149..80631f50 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,6 +16,8 @@ eval:
# conda config --add channels conda-forge
#- conda config --add channels bioconda
#- conda config --add channels mandiayba
+ - ln -s /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/ancillaries/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
+ - ls ancillaries/extended-microorganisms-taxonomy
- conda activate snakemake-7.5.0
- snakemake --help
- pwd
--
GitLab
From 56173c04c5c44e2831d740e9f31d99d9986de096 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 15:34:43 +0100
Subject: [PATCH 02/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 80631f50..df0e7b8d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,7 +16,7 @@ eval:
# conda config --add channels conda-forge
#- conda config --add channels bioconda
#- conda config --add channels mandiayba
- - ln -s /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/ancillaries/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
+ - cp -r /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/ancillaries/extended-microorganisms-taxonomy ancillaries/
- ls ancillaries/extended-microorganisms-taxonomy
- conda activate snakemake-7.5.0
- snakemake --help
--
GitLab
From a18ce81d524e5f057eb810cfa6bca2da4fa6af10 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 15:40:23 +0100
Subject: [PATCH 03/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index df0e7b8d..0a26ea93 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,14 +16,14 @@ eval:
# conda config --add channels conda-forge
#- conda config --add channels bioconda
#- conda config --add channels mandiayba
- - cp -r /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/ancillaries/extended-microorganisms-taxonomy ancillaries/
+ - ln /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- conda activate snakemake-7.5.0
- snakemake --help
- pwd
- ls -l
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile process-evaluate_BioNLP-OST.snakefile all
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12"
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12"
artifacts:
paths:
- corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json
--
GitLab
From 4e3f6ccc6031419102ab726fcb9ad9aae2ab0d92 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 15:41:01 +0100
Subject: [PATCH 04/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0a26ea93..51cd8f5e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,7 +16,7 @@ eval:
# conda config --add channels conda-forge
#- conda config --add channels bioconda
#- conda config --add channels mandiayba
- - ln /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
+ - ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- conda activate snakemake-7.5.0
- snakemake --help
--
GitLab
From 43769f3886157152da4d676436f27107009ae4ac Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 15:43:40 +0100
Subject: [PATCH 05/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 51cd8f5e..423ac060 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,11 +19,8 @@ eval:
- ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- conda activate snakemake-7.5.0
- - snakemake --help
- - pwd
- - ls -l
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12"
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12"
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --dryrun
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --dryrun
artifacts:
paths:
- corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json
--
GitLab
From a93b1072936ac8cbe33a6bcfb94cafb3df7d37ee Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 15:51:00 +0100
Subject: [PATCH 06/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 423ac060..93a0b839 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,8 +19,8 @@ eval:
- ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- conda activate snakemake-7.5.0
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --dryrun
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --dryrun
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" #--dryrun
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" #--dryrun
artifacts:
paths:
- corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json
--
GitLab
From b56711648ac4a93811bc5dc656bfc122aa361cfa Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 16:06:15 +0100
Subject: [PATCH 07/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 93a0b839..79749ad1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,8 +19,8 @@ eval:
- ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- conda activate snakemake-7.5.0
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" #--dryrun
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" #--dryrun
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
paths:
- corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json
--
GitLab
From b70fd547ade7f190027df47f207e4bb63b6be01c Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 16:57:02 +0100
Subject: [PATCH 08/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 79749ad1..86d78a33 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,7 +18,9 @@ eval:
#- conda config --add channels mandiayba
- ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- - conda activate snakemake-7.5.0
+ - conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
+ - conda activate snakemake-5.13.0-env
+ #- conda activate snakemake-7.5.0
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
--
GitLab
From c7f5749a6447519c66d13e8f519c942542e39596 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 17:02:42 +0100
Subject: [PATCH 09/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 86d78a33..ea46cd34 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,9 +18,9 @@ eval:
#- conda config --add channels mandiayba
- ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- - conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
- - conda activate snakemake-5.13.0-env
- #- conda activate snakemake-7.5.0
+ #- conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
+ #- conda activate snakemake-5.13.0-env
+ - conda activate snakemake-7.5.0
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
--
GitLab
From fe7c1e8922f42ff25b60fa3c53b20fc47ee5e3bc Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 17:21:49 +0100
Subject: [PATCH 10/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ea46cd34..7bdf851d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ eval:
#- conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
#- conda activate snakemake-5.13.0-env
- conda activate snakemake-7.5.0
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
paths:
--
GitLab
From a68fbb2b65950a18855daa139d16e178e99d83a9 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 17:44:52 +0100
Subject: [PATCH 11/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7bdf851d..93aae0c5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ eval:
#- conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
#- conda activate snakemake-5.13.0-env
- conda activate snakemake-7.5.0
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
+ - snakemake --nolock --use-singularity --use-conda --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
paths:
--
GitLab
From d87a22917c42a936ac879d4fc257147a8a323a6e Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Tue, 6 Dec 2022 17:53:34 +0100
Subject: [PATCH 12/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 93aae0c5..c9e603f1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ eval:
#- conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
#- conda activate snakemake-5.13.0-env
- conda activate snakemake-7.5.0
- - snakemake --nolock --use-singularity --use-conda --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
paths:
--
GitLab
From 866b6710cfde047f71b9c7c72b0df1affb2c2c8a Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 7 Dec 2022 08:49:14 +0100
Subject: [PATCH 13/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c9e603f1..5b6265c1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,9 +18,9 @@ eval:
#- conda config --add channels mandiayba
- ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- #- conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
- #- conda activate snakemake-5.13.0-env
- - conda activate snakemake-7.5.0
+ - conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
+ - conda activate snakemake-5.13.0-env
+ #- conda activate snakemake-7.5.0
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
--
GitLab
From 02679f28380ce53855d9c0fc5e9ac996d80adb6f Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 7 Dec 2022 09:37:26 +0100
Subject: [PATCH 14/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5b6265c1..7bdf851d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,10 +18,10 @@ eval:
#- conda config --add channels mandiayba
- ln -s /projet/tmp/extended-microorganisms-taxonomy ancillaries/extended-microorganisms-taxonomy
- ls ancillaries/extended-microorganisms-taxonomy
- - conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
- - conda activate snakemake-5.13.0-env
- #- conda activate snakemake-7.5.0
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
+ #- conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
+ #- conda activate snakemake-5.13.0-env
+ - conda activate snakemake-7.5.0
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
paths:
--
GitLab
From 12148b22bb418f1a476fae0c996303b99cc5d8c3 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 7 Dec 2022 09:53:17 +0100
Subject: [PATCH 15/17] Update preprocess-ontology.snakefile
---
preprocess-ontology.snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/preprocess-ontology.snakefile b/preprocess-ontology.snakefile
index 17a33b93..51be913f 100644
--- a/preprocess-ontology.snakefile
+++ b/preprocess-ontology.snakefile
@@ -40,7 +40,7 @@ rule remove_obsolete_concepts:
output:
onto='ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo'
conda: 'softwares/envs/obo-utils-env.yaml'
- shell: 'python softwares/obo-utils/obo2obo.py {input.onto} > {output.onto}'
+ shell: 'python2 softwares/obo-utils/obo2obo.py {input.onto} > {output.onto}'
'''
--
GitLab
From f522e64b66a6677146ce36074c2aad4331b00f26 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 7 Dec 2022 10:43:14 +0100
Subject: [PATCH 16/17] Update .gitlab-ci.yml file
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7bdf851d..5bdcf4fa 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,7 +21,7 @@ eval:
#- conda env create -f softwares/envs/snakemake-5.13.0-env.yaml
#- conda activate snakemake-5.13.0-env
- conda activate snakemake-7.5.0
- - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
+ - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 1 --snakefile preprocess-ontology.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q short.q,long.q -pe thread 12" --restart-times 2
- snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 10 --snakefile process-evaluate_BioNLP-OST.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=36G -V -cwd -e log/ -o log/ -q bigmem.q,highmem.q -pe thread 12" --restart-times 2
artifacts:
paths:
--
GitLab
From 9b2752b8048e7b638152e134104d6df59ea04a7b Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 7 Dec 2022 11:36:07 +0100
Subject: [PATCH 17/17] Update preprocess-ontology.snakefile
---
preprocess-ontology.snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/preprocess-ontology.snakefile b/preprocess-ontology.snakefile
index 51be913f..17a33b93 100644
--- a/preprocess-ontology.snakefile
+++ b/preprocess-ontology.snakefile
@@ -40,7 +40,7 @@ rule remove_obsolete_concepts:
output:
onto='ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo'
conda: 'softwares/envs/obo-utils-env.yaml'
- shell: 'python2 softwares/obo-utils/obo2obo.py {input.onto} > {output.onto}'
+ shell: 'python softwares/obo-utils/obo2obo.py {input.onto} > {output.onto}'
'''
--
GitLab