diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ea7c4746a862a5e985bc29f42d7d2c674f6b88dc..39af81496d2214e8c175f745110e9b2e4e4baa85 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,26 +1,25 @@ -image: mandiayba/migale-base +#image: mandiayba/migale-base -stages: - - deploy - - -# install ressources +# eval eval: - stage: deploy - script: + tags: + - migale + script: - cd softwares/ - - singularity pull library://migale/default/alvisnlp:0.8.1 - - ln -s $PWD/alvisnlp_0.8.1.sif alvisnlp.sif + #- singularity pull library://migale/default/alvisnlp:0.8.1 + - ln -s /work_projet/bibliome/singularity/alvisnlp_0.8.1.sif alvisnlp_0.8.1.sif + #- ln -s $PWD/alvisnlp_0.8.1.sif alvisnlp.sif - git clone https://github.com/Bibliome/obo-utils.git - cd .. - - conda init bash - - source /usr/local/etc/profile.d/conda.sh - - conda config --add channels conda-forge - - conda config --add channels bioconda - - conda config --add channels mandiayba - - conda activate snakemake-7.5.0-env - - conda install -c conda-forge mamba + #- conda init bash + #- source /usr/local/etc/profile.d/conda.sh + # conda config --add channels conda-forge + #- conda config --add channels bioconda + #- conda config --add channels mandiayba + - 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 artifacts: diff --git a/config/config.yaml b/config/config.yaml index e66098d88124530b40ba6636b121d36c8d06e5f1..b49f1e5ae9e0e0ccf438fe9f3068aae762b35ada 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -1,7 +1,7 @@ # params value # TMP -TMP: "/work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/tmp/" +TMP: "/tmp/" # ontobiotope ONTOBIOTOPE: "ancillaries/BioNLP-OST+EnovFood.obo" diff --git a/preprocess-ontology.snakefile b/preprocess-ontology.snakefile index 529e6f0667cda76de3f3c6e1c3c184eda491eb30..17a33b930dbd26eef4c1b78f527aba187922abcc 100644 --- a/preprocess-ontology.snakefile +++ b/preprocess-ontology.snakefile @@ -130,7 +130,7 @@ rule analyze_onto_phenotype: tmpDir=config['TMP'] singularity:config["SINGULARITY_IMG"] shell: """ - alvisnlp -J-Xmx8g -tmp {params.tmpDir} -verbose \ + alvisnlp -J-Xmx8g -cleanTmp -tmp {params.tmpDir} -verbose \ -alias input {input.onto} \ -alias output {output.tomap} \ {params.plan}