From 7a4597b7f180be53aab4461671a678e90ad73d47 Mon Sep 17 00:00:00 2001 From: David Waite Date: Tue, 1 Jul 2025 09:03:19 +1200 Subject: [PATCH] Added tmp directory flags missing subroutines The --tmpdir flag was not invoked for the palm_hmm_motif_search.py, palm_hmm_search.py, or palm_diamond_motif_search.py scripts causing them to write to /tmp/ even when the user specified a custom temporary directory. --- py/palm_annot.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/py/palm_annot.py b/py/palm_annot.py index c9d87e0..7cc7430 100644 --- a/py/palm_annot.py +++ b/py/palm_annot.py @@ -183,22 +183,25 @@ def MakeTmp(Name): Exec(CmdLine) CmdLine = RepoDir + "py/palm_hmm_motif_search.py" -CmdLine += " --input " + AaFN +CmdLine += " --input " + AaFN CmdLine += " --fev " + HMM_motif_fev +CmdLine += " --tmpdir " + TmpDir if not Args.threads is None: CmdLine += " --threads %d" % Args.threads Exec(CmdLine) CmdLine = RepoDir + "py/palm_hmm_search.py" -CmdLine += " --input " + AaFN -CmdLine += " --fev " + HMM_pm_fev +CmdLine += " --input " + AaFN +CmdLine += " --fev " + HMM_pm_fev +CmdLine += " --tmpdir " + TmpDir if not Args.threads is None: CmdLine += " --threads %d" % Args.threads Exec(CmdLine) CmdLine = RepoDir + "py/palm_diamond_motif_search.py" -CmdLine += " --input " + AaFN +CmdLine += " --input " + AaFN CmdLine += " --fev " + Dmnd_fev +CmdLine += " --tmpdir " + TmpDir if not Args.threads is None: CmdLine += " --threads %d" % Args.threads Exec(CmdLine)