From 1838f3ffa0e1e3537728255949d55cb94154e69f Mon Sep 17 00:00:00 2001 From: gordonkoehn Date: Wed, 30 Aug 2023 09:42:02 +0200 Subject: [PATCH 1/2] setup mark03 --- workflows/mark03.smk | 6 +++--- workflows/tree_inference.smk | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/workflows/mark03.smk b/workflows/mark03.smk index bf6bdfe8..e9cc51e1 100644 --- a/workflows/mark03.smk +++ b/workflows/mark03.smk @@ -17,8 +17,8 @@ from pyggdrasil.tree_inference import CellSimulationId, TreeType, TreeId, McmcCo ##################### # Environment variables -DATADIR = "../data" -#DATADIR = "/cluster/work/bewi/members/gkoehn/data" +#DATADIR = "../data" +DATADIR = "/cluster/work/bewi/members/gkoehn/data" ##################### experiment = "mark03" @@ -64,7 +64,7 @@ CS_seed = 42 # <-- configure cell simulation seed here ##################### # True Tree Parameters tree_types = ["r"] # <-- configure tree type here ["r","s","d"] -tree_seeds = [42] # <-- configure tree seed here +tree_seeds = [42,34] # <-- configure tree seed here ##################### ##################### diff --git a/workflows/tree_inference.smk b/workflows/tree_inference.smk index 918ee7f7..e0eaa445 100644 --- a/workflows/tree_inference.smk +++ b/workflows/tree_inference.smk @@ -19,9 +19,9 @@ from pyggdrasil.tree_inference import ( ############################################### ## Relative path from DATADIR to the repo root -#REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil" -REPODIR = ".." -#DATADIR = "/cluster/work/bewi/members/gkoehn/data" +REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil" +#REPODIR = ".." +DATADIR = "/cluster/work/bewi/members/gkoehn/data" ############################################### From 643a06e96ae6d632c349a7bc8354a754ddbf5e55 Mon Sep 17 00:00:00 2001 From: gordonkoehn Date: Thu, 31 Aug 2023 17:23:20 +0200 Subject: [PATCH 2/2] =?UTF-8?q?remove=20MP=C2=A7?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- workflows/mark03.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/mark03.smk b/workflows/mark03.smk index e9cc51e1..ca3099b5 100644 --- a/workflows/mark03.smk +++ b/workflows/mark03.smk @@ -24,7 +24,7 @@ DATADIR = "/cluster/work/bewi/members/gkoehn/data" experiment = "mark03" # Metrics: Distances / Similarity Measure to use -metrics = ["MP3", "AD", "log_prob", "DL"] # <-- configure distances here +metrics = ["AD", "log_prob", "DL"] # also MP3 <-- configure distances here ##################### # Error Parameters