Make Gemma's appdata directory configurable

PavlidisLab · May 17, 2024 · ac1da2a · ac1da2a
1 parent acf0e84
commit ac1da2a
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Showing 3 changed files with 3 additions and 1 deletion.
diff --git a/example.luigi.cfg b/example.luigi.cfg
@@ -58,6 +58,7 @@ GEMMA_BASEURL=https://gemma.msl.ubc.ca
 SLACK_WEBHOOK_URL=
 
 [rnaseq_pipeline.gemma]
+appdata_dir=/space/gemmaData
 human_reference_id=hg38_ncbi
 mouse_reference_id=mm10_ncbi
 rat_reference_id=rn7_ncbi

diff --git a/rnaseq_pipeline/gemma.py b/rnaseq_pipeline/gemma.py
@@ -12,6 +12,7 @@
 
 class gemma(luigi.Config):
     task_namespace = 'rnaseq_pipeline'
+    appdata_dir = luigi.Parameter()
     human_reference_id = luigi.Parameter()
     mouse_reference_id = luigi.Parameter()
     rat_reference_id = luigi.Parameter()

diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py
@@ -441,7 +441,7 @@ def run(self):
         copytree(dirname(self.input().path), dirname(self.output().path), dirs_exist_ok=True)
 
     def output(self):
-       return luigi.LocalTarget(f'/space/gemmaData/metadata/{self.experiment_id}/MultiQCReports/multiqc_report.html')
+       return luigi.LocalTarget(join(gemma_cfg.appdata_dir, 'metadata', self.experiment_id, 'MultiQCReports/multiqc_report.html'))
 
 @requires(SubmitExperimentDataToGemma, SubmitExperimentBatchInfoToGemma, SubmitExperimentReportToGemma)
 class SubmitExperimentToGemma(TaskWithOutputMixin, WrapperTask):