From efded24ac5b1dfc45c14ec1e8c812cff4cc09416 Mon Sep 17 00:00:00 2001 From: TBradley27 Date: Thu, 16 May 2019 21:51:06 +0100 Subject: [PATCH] use travis_wait tag for some commands --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 723d115..c4730e6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -24,7 +24,7 @@ install: - conda config --add channels r - conda config --add channels conda-forge - conda config --add channels bioconda - - conda create -q -n test-environment snakemake r r-devtools perl-app-cpanminus python=$TRAVIS_PYTHON_VERSION + - travis_wait conda create -q -n test-environment snakemake r r-devtools perl-app-cpanminus python=$TRAVIS_PYTHON_VERSION script: - source activate test-environment @@ -33,7 +33,7 @@ script: - cpanm Statistics::Lite - Rscript -e 'devtools::install_github("TBradley27/filtar_R")' - snakemake --version - - snakemake --use-conda -p results/targets/mmu/oocyte_chrY.contextpp.tsv --config sequence_data_source=SRA conservation=False reannotation=False mirnas="['mmu-miR-188-5p']" transcripts="['ENSMUST00000189888.6']" TPM_expression_threshold=0 prediction_algorithm=TargetScan7 && head results/targets/mmu/oocyte_chrY.contextpp.tsv && rm -f results/targets/mmu/oocyte_chrY.contextpp.tsv ## create empty target for downstream command + - travis_wait 50 snakemake --use-conda -p results/targets/mmu/oocyte_chrY.contextpp.tsv --config sequence_data_source=SRA conservation=False reannotation=False mirnas="['mmu-miR-188-5p']" transcripts="['ENSMUST00000189888.6']" TPM_expression_threshold=0 prediction_algorithm=TargetScan7 && head results/targets/mmu/oocyte_chrY.contextpp.tsv && rm -f results/targets/mmu/oocyte_chrY.contextpp.tsv ## create empty target for downstream command - snakemake --use-conda -p results/targets/miRanda/mmu/oocyte/chrY.tsv --config sequence_data_source=SRA conservation=False reannotation=False mirnas="['mmu-miR-188-5p']" transcripts="['ENSMUST00000189888.6']" TPM_expression_threshold=0 prediction_algorithm=miRanda - head results/targets/miRanda/mmu/oocyte/chrY.tsv - snakemake --use-conda -p results/targets/mmu/oocyte_chrY.contextpp.tsv --config sequence_data_source=SRA conservation=True reannotation=False mirnas="['mmu-miR-188-5p']" transcripts="['ENSMUST00000189888.6']" TPM_expression_threshold=0 prediction_algorithm=TargetScan7