From 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5 Mon Sep 17 00:00:00 2001 From: Benjamin Dartigues Date: Fri, 21 Jun 2024 20:31:00 +0200 Subject: [PATCH] =?UTF-8?q?rename=20all=20config=20dirs=20to=20avoid=20con?= =?UTF-8?q?flicts=20when=20running=20parallel=20tasks=E2=80=A6=20(#6041)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * rename all config dirs to avoid conflicts when running parallel tasks in galaxy workflow * upgrade tool version suffix * Update macros.xml * Update dimet_timecourse_analysis.xml * Update dimet_pca_plot.xml * Update dimet_pca_analysis.xml * Update dimet_pca_analysis.xml * Update dimet_metabologram.xml * Update dimet_metabologram.xml * Update dimet_isotopologues_plot.xml * Update dimet_isotopologues_plot.xml * Update dimet_enrichment_plot.xml * Update dimet_differential_multigroup_analysis.xml * Update dimet_differential_multigroup_analysis.xml * Update dimet_differential_analysis.xml * Update dimet_bivariate_analysis.xml * Update dimet_abundance_plot.xml * replace __new_file_path__ by temp directory in job working directory * replace back temp by __new_file_path__ directory in job working directory * replace back temp by __new_file_path__ directory in job working directory * put back the ./config dir in macros.xml, remoce -cp option in hydra args and replace ++hydra.run.dir=XXXXX by ++hydra.run.dir=. --------- Co-authored-by: M Bernt --- tools/dimet/dimet_abundance_plot.xml | 5 ++--- tools/dimet/dimet_bivariate_analysis.xml | 5 ++--- tools/dimet/dimet_differential_analysis.xml | 5 ++--- tools/dimet/dimet_differential_multigroup_analysis.xml | 5 ++--- tools/dimet/dimet_enrichment_plot.xml | 5 ++--- tools/dimet/dimet_isotopologues_plot.xml | 5 ++--- tools/dimet/dimet_metabologram.xml | 5 ++--- tools/dimet/dimet_pca_analysis.xml | 5 ++--- tools/dimet/dimet_pca_plot.xml | 6 ++---- tools/dimet/dimet_timecourse_analysis.xml | 3 +-- tools/dimet/macros.xml | 9 ++++----- 11 files changed, 23 insertions(+), 35 deletions(-) diff --git a/tools/dimet/dimet_abundance_plot.xml b/tools/dimet/dimet_abundance_plot.xml index 28db40fb6ed..11a45025ef6 100644 --- a/tools/dimet/dimet_abundance_plot.xml +++ b/tools/dimet/dimet_abundance_plot.xml @@ -15,8 +15,7 @@ @INIT_TIMEPOINTS@ @INIT_ENRICHMENT_METABOLITES@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=abundance_plot' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -232,4 +231,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_bivariate_analysis.xml b/tools/dimet/dimet_bivariate_analysis.xml index 67663d082ad..f779ba787e9 100644 --- a/tools/dimet/dimet_bivariate_analysis.xml +++ b/tools/dimet/dimet_bivariate_analysis.xml @@ -13,8 +13,7 @@ @INIT_BI_ANALYSIS@ @INIT_BIVAR_COMPARISONS@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=bivariate_analysis' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -272,4 +271,4 @@ You can also use the minimal data examples from https://zenodo.org/records/10579 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_differential_analysis.xml b/tools/dimet/dimet_differential_analysis.xml index c2010338530..cd6e011860d 100644 --- a/tools/dimet/dimet_differential_analysis.xml +++ b/tools/dimet/dimet_differential_analysis.xml @@ -15,8 +15,7 @@ @INIT_GROUPS@ @INIT_DIFF_ANALYSIS_COMPARISONS@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=differential_analysis' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -305,4 +304,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_differential_multigroup_analysis.xml b/tools/dimet/dimet_differential_multigroup_analysis.xml index 371db85ef6d..3d51ed28a92 100644 --- a/tools/dimet/dimet_differential_multigroup_analysis.xml +++ b/tools/dimet/dimet_differential_multigroup_analysis.xml @@ -17,8 +17,7 @@ @INIT_TIMEPOINTS@ @INIT_MULTIGROUP_COMPARISONS@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=multi_group_comparison' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -262,4 +261,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_enrichment_plot.xml b/tools/dimet/dimet_enrichment_plot.xml index 63c09366d2a..768d2271122 100644 --- a/tools/dimet/dimet_enrichment_plot.xml +++ b/tools/dimet/dimet_enrichment_plot.xml @@ -15,8 +15,7 @@ @INIT_TIMEPOINTS@ @INIT_ENRICHMENT_METABOLITES@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=mean_enrichment_line_plot' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -242,4 +241,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_isotopologues_plot.xml b/tools/dimet/dimet_isotopologues_plot.xml index 7808cd2ba0a..550cf74e627 100644 --- a/tools/dimet/dimet_isotopologues_plot.xml +++ b/tools/dimet/dimet_isotopologues_plot.xml @@ -14,8 +14,7 @@ @INIT_PLOT_CONDITIONS@ @INIT_TIMEPOINTS@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=isotopologue_proportions_plot' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -254,4 +253,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_metabologram.xml b/tools/dimet/dimet_metabologram.xml index def017a42b1..fdf6f59a583 100644 --- a/tools/dimet/dimet_metabologram.xml +++ b/tools/dimet/dimet_metabologram.xml @@ -16,10 +16,9 @@ @INIT_PATHWAYS@ @INIT_STAT_TEST@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' - '++hydra.run.dir=metabologram' '++analysis={ dataset:{ _target_: dimet.data.DataIntegrationConfig, @@ -344,4 +343,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_pca_analysis.xml b/tools/dimet/dimet_pca_analysis.xml index 741694fe42e..0bcf60f1dc4 100644 --- a/tools/dimet/dimet_pca_analysis.xml +++ b/tools/dimet/dimet_pca_analysis.xml @@ -14,8 +14,7 @@ @INIT_IMPUTE_VALUES@ @INIT_CONDITIONS@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=pca-analysis-tables' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -212,4 +211,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_pca_plot.xml b/tools/dimet/dimet_pca_plot.xml index 9729c90de9b..317da2487b2 100644 --- a/tools/dimet/dimet_pca_plot.xml +++ b/tools/dimet/dimet_pca_plot.xml @@ -14,8 +14,7 @@ @INIT_IMPUTE_VALUES@ @INIT_CONDITIONS@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' - '++hydra.run.dir=pca-plot' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' '++analysis={ @@ -50,7 +49,6 @@ '++analysis.dataset.mean_enrichment=me_or_frac_contrib' #end if @REMOVE_CONFIG@ - ]]> @@ -240,4 +238,4 @@ You can also use the minimal data examples from https://zenodo.org/record/105798 ]]> - \ No newline at end of file + diff --git a/tools/dimet/dimet_timecourse_analysis.xml b/tools/dimet/dimet_timecourse_analysis.xml index 6d3cf80255c..e37d0925f3d 100644 --- a/tools/dimet/dimet_timecourse_analysis.xml +++ b/tools/dimet/dimet_timecourse_analysis.xml @@ -15,10 +15,9 @@ @INIT_GROUPS@ @INIT_CONDITIONS_TIMECOURSE@ HYDRA_FULL_ERROR=1 python -m dimet - -cp '$__new_file_path__/config' + '++hydra.run.dir=.' '++figure_path=figures' '++table_path=tables' - '++hydra.run.dir=time_course_analysis' '++analysis={ dataset:{ _target_: dimet.data.DatasetConfig, diff --git a/tools/dimet/macros.xml b/tools/dimet/macros.xml index ff12557a246..b280795bafe 100644 --- a/tools/dimet/macros.xml +++ b/tools/dimet/macros.xml @@ -1,6 +1,6 @@ 0.2.4 - 2 + 3 dimet @@ -598,16 +598,15 @@ ]]>