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Commit 79ce276d authored by Yohan Jarosz's avatar Yohan Jarosz
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fix gilab ci

parent 6346ff4f
Pipeline #1704 canceled with stages
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      .gitlab-ci.yml
      View file @ 79ce276d
      ...@@ -15,7 +15,7 @@ databases: ...@@ -15,7 +15,7 @@ databases:
      - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d $CI_PROJECT_DIR/$CI_BUILD_ID init - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d $CI_PROJECT_DIR/$CI_BUILD_ID init
      # INIT # INIT
      # i-cl: # i-cl:
      # stage: init # stage: init
      # script: # script:
      ...@@ -75,13 +75,13 @@ databases: ...@@ -75,13 +75,13 @@ databases:
      # dag-mg-nf2: # dag-mg-nf2:
      # stage: dag # stage: dag
      # script: # script:
      - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n" --no-filtering # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n" --no-filtering
      # dag-mt-default: # dag-mt-default:
      # stage: dag # stage: dag
      # script: # script:
      - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n" # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
      # dag-mt-nf: # dag-mt-nf:
      ...@@ -121,7 +121,7 @@ databases: ...@@ -121,7 +121,7 @@ databases:
      # p-mgmt-default: # p-mgmt-default:
      # stage: preprocessing # stage: preprocessing
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
      ...@@ -129,7 +129,7 @@ databases: ...@@ -129,7 +129,7 @@ databases:
      # p-mgmt-nf: # p-mgmt-nf:
      # stage: preprocessing # stage: preprocessing
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
      ...@@ -143,21 +143,21 @@ databases: ...@@ -143,21 +143,21 @@ databases:
      # p-mg-nf: # p-mg-nf:
      # stage: preprocessing # stage: preprocessing
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics --single-step # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics --single-step
      # p-mt-default: # p-mt-default:
      # stage: preprocessing # stage: preprocessing
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics --single-step # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics --single-step
      # p-mt-nf: # p-mt-nf:
      # stage: preprocessing # stage: preprocessing
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics --single-step # - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics --single-step
      ...@@ -166,7 +166,7 @@ databases: ...@@ -166,7 +166,7 @@ databases:
      # stage: manual # stage: manual
      # when: manual # when: manual
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
      ...@@ -174,33 +174,33 @@ databases: ...@@ -174,33 +174,33 @@ databases:
      # stage: manual # stage: manual
      # when: manual # when: manual
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
      # a-mt-idba: # a-mt-idba:
      # stage: manual # stage: manual
      # when: manual # when: manual
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
      # a-mgmt-megahit: # a-mgmt-megahit:
      # stage: assembly # stage: assembly
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
      # a-mg-megahit: # a-mg-megahit:
      # stage: assembly # stage: assembly
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
      # a-mt-megahit: # a-mt-megahit:
      # stage: assembly # stage: assembly
      # script: # script:
      # - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
      ...@@ -232,7 +232,7 @@ an-mt: ...@@ -232,7 +232,7 @@ an-mt:
      # binny-mgmt: # binny-mgmt:
      # stage: binning # stage: binning
      # script: # script:
      - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID # - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
      # - cp -r /mnt/data/input/binny-mgmt/* $CI_PROJECT_DIR/$CI_BUILD_ID # - cp -r /mnt/data/input/binny-mgmt/* $CI_PROJECT_DIR/$CI_BUILD_ID
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db binning --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db binning --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
      ...@@ -240,7 +240,7 @@ an-mt: ...@@ -240,7 +240,7 @@ an-mt:
      # binny-mg: # binny-mg:
      # stage: binning # stage: binning
      # script: # script:
      - pip3.4 install --editable . --user # - pip3.4 install --editable . --user
      # - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID # - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
      # - cp -r /mnt/data/input/binny-mg/* $CI_PROJECT_DIR/$CI_BUILD_ID # - cp -r /mnt/data/input/binny-mg/* $CI_PROJECT_DIR/$CI_BUILD_ID
      # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db binning --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics # - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db binning --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
      ......
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