From 8332bba137713cf02150fe6464b847f9c45fb5b9 Mon Sep 17 00:00:00 2001 From: bio-la Date: Mon, 4 Mar 2024 15:38:07 +0100 Subject: [PATCH 1/5] changes to accomodate different mem threads --- panpipes/panpipes/pipeline_refmap.py | 15 ++++++++++++--- panpipes/panpipes/pipeline_refmap/pipeline.yml | 2 +- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/panpipes/panpipes/pipeline_refmap.py b/panpipes/panpipes/pipeline_refmap.py index 5ee59289..f9481224 100644 --- a/panpipes/panpipes/pipeline_refmap.py +++ b/panpipes/panpipes/pipeline_refmap.py @@ -9,7 +9,7 @@ from itertools import chain import glob -# __file__="/well/cartography/users/zsj686/non_cart_projects/005-multimodal_scpipelines/src/sc_pipelines_muon_dev/panpipes/pipeline_refmap.py" + PARAMS = P.get_parameters( ["%s/pipeline.yml" % os.path.splitext(__file__)[0], "pipeline.yml"]) @@ -104,7 +104,16 @@ def run_refmap_scvi(infile, outfile, log_file, ref_architecture ): cmd += " --predict_rf %(run_randomforest)s" cmd += " > %(log_file)s" - job_kwargs["job_threads"] = PARAMS['resources_threads_low'] + + if PARAMS['queues_gpu'] is not None: + job_kwargs["job_queue"] = PARAMS['queues_gpu'] + job_kwargs["job_threads"] = int(PARAMS['resources_threads_gpu']) + elif PARAMS['queues_long'] is not None: + job_kwargs["job_queue"] = job_queue=PARAMS['queues_long'] + job_kwargs["job_threads"] = int(PARAMS['resources_threads_high']) + else: + job_kwargs["job_threads"] = int(PARAMS['resources_threads_high']) + P.run(cmd, **job_kwargs) @@ -150,7 +159,7 @@ def run_scib_refmap(infile,logfile): if PARAMS['query_celltype'] is not None: cmd += " --covariate %(query_celltype)s" cmd += " > %(logfile)s" - job_kwargs["job_threads"] = PARAMS['resources_threads_medium'] + job_kwargs["job_threads"] = PARAMS['resources_threads_high'] P.run(cmd, **job_kwargs) diff --git a/panpipes/panpipes/pipeline_refmap/pipeline.yml b/panpipes/panpipes/pipeline_refmap/pipeline.yml index e94b63ab..d82a4206 100644 --- a/panpipes/panpipes/pipeline_refmap/pipeline.yml +++ b/panpipes/panpipes/pipeline_refmap/pipeline.yml @@ -18,7 +18,7 @@ resources: condaenv: # allows for tweaking which queues jobs get submitted to, -# in case there is a special queue for long jobs or you have access to a gpu-sepcific queue +# in case there is a special queue for long jobs or you have access to a gpu-specific queue # the default queue should be specified in your .cgat.yml file # leave as is if you do not want to use the alternative queues queues: From c06a656520abfcab8cd3ef2a42b65375c2f72f66 Mon Sep 17 00:00:00 2001 From: bio-la Date: Mon, 4 Mar 2024 15:42:21 +0100 Subject: [PATCH 2/5] changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dce3d798..d81a1683 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,9 @@ ### fixed - fixed error in `vis` - - error occurred when only wanting to plot continuous or categorical variables (or neither), not both + - error occurred when only wanting to plot continuous or categorical variables (or neither), not both +- fixed error in `refmap` + - high threads was not recognised, now fixed. ### dependencies From e6921d79db15dad206e62daf033d842ce222c769 Mon Sep 17 00:00:00 2001 From: bio-la Date: Mon, 4 Mar 2024 15:42:38 +0100 Subject: [PATCH 3/5] release --- docs/release_notes.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/release_notes.md b/docs/release_notes.md index dce3d798..d81a1683 100644 --- a/docs/release_notes.md +++ b/docs/release_notes.md @@ -10,7 +10,9 @@ ### fixed - fixed error in `vis` - - error occurred when only wanting to plot continuous or categorical variables (or neither), not both + - error occurred when only wanting to plot continuous or categorical variables (or neither), not both +- fixed error in `refmap` + - high threads was not recognised, now fixed. ### dependencies From 4fd43e9c9de7130a3e2f4ee1e4c4337c1ea14693 Mon Sep 17 00:00:00 2001 From: bio-la Date: Mon, 4 Mar 2024 15:43:49 +0100 Subject: [PATCH 4/5] python --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d81a1683..5df8f10a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,8 @@ - high threads was not recognised, now fixed. ### dependencies +- All the dependencies have been updated. + - Python>=3.10 required ## v0.4.1 From f3bf7b816e1d3d168cbced7102d0cc24a38b88ea Mon Sep 17 00:00:00 2001 From: bio-la Date: Mon, 4 Mar 2024 15:43:58 +0100 Subject: [PATCH 5/5] release notes --- docs/release_notes.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/release_notes.md b/docs/release_notes.md index d81a1683..5df8f10a 100644 --- a/docs/release_notes.md +++ b/docs/release_notes.md @@ -15,6 +15,8 @@ - high threads was not recognised, now fixed. ### dependencies +- All the dependencies have been updated. + - Python>=3.10 required ## v0.4.1