From 542f6794648877081e8aed02987b8f175443d41e Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Fri, 2 Aug 2024 11:42:53 -0700
Subject: [PATCH] Remove $$() construct from condor submission scripts

I apparently misunderstood it's use according to more recent
documentation $$() is for looking up classad variables and not
submission script variables.

Though hopefully the $(variable:default) construct works, as that's
what I had been using $$($(variable):default) for
---
 woldrnaseq/align-star.condor            | 9 +++++----
 woldrnaseq/bam2bigwig_stranded.condor   | 2 +-
 woldrnaseq/bam2bigwig_unstranded.condor | 2 +-
 woldrnaseq/qc-coverage.condor           | 6 +++---
 woldrnaseq/qc-distribution.condor       | 6 +++---
 woldrnaseq/qc-flagstat.condor           | 4 ++--
 woldrnaseq/qc-samstats.condor           | 6 +++---
 woldrnaseq/quant-rsem.condor            | 4 ++--
 woldrnaseq/rrna-premap.condor           | 2 +-
 woldrnaseq/sort-samtools.condor         | 2 +-
 10 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/woldrnaseq/align-star.condor b/woldrnaseq/align-star.condor
index ee28ba2..a3ff754 100644
--- a/woldrnaseq/align-star.condor
+++ b/woldrnaseq/align-star.condor
@@ -1,17 +1,18 @@
 universe=vanilla
+CURDIR=$(curdir)
+
 log=$(CURDIR)/align-star-$(Process).log
 output=$(CURDIR)/align-star-$(Process).out
 error=$(CURDIR)/align-star-$(Process).out
 
 STAR_DIR=$(star_dir)
-GENOME_ROOT=$$($(genome_root):/woldlab/castor/home/diane/proj/genome)
+GENOME_ROOT=$($(genome_root:/woldlab/castor/home/diane/proj/genome)
 GENOME_NAME=$(GENOME_NAME)
 GENOME_DIR=$(GENOME_ROOT)/$(GENOME_NAME)/
 THREADS=8
 
-READ1=$$(read1)
-READ2=$$(read2:)
-CURDIR=$$(curdir)
+READ1=$(read1)
+READ2=$(read2:)
 
 if defined READ2
   EXTRA_ARGS=
diff --git a/woldrnaseq/bam2bigwig_stranded.condor b/woldrnaseq/bam2bigwig_stranded.condor
index 7cd2962..bec2cba 100644
--- a/woldrnaseq/bam2bigwig_stranded.condor
+++ b/woldrnaseq/bam2bigwig_stranded.condor
@@ -6,7 +6,7 @@ log=$(curdir)/bam2bigwig-$(Process).log
 output=$(curdir)/bam2bigwig-$(Process).out
 error=$(curdir)/bam2bigwig-$(Process).out
 
-ANALYSIS_NAME=$$($(analysis_name):Analysis)
+ANALYSIS_NAME=$(analysis_name:Analysis)
 
 GENOME_NAME=$(GENOME_NAME)
 IN=$(ANALYSIS_NAME)-$(GENOME_NAME)_genome.bam
diff --git a/woldrnaseq/bam2bigwig_unstranded.condor b/woldrnaseq/bam2bigwig_unstranded.condor
index dbec98a..a95bb34 100644
--- a/woldrnaseq/bam2bigwig_unstranded.condor
+++ b/woldrnaseq/bam2bigwig_unstranded.condor
@@ -7,7 +7,7 @@ output=$(curdir)/bam2bigwig-$(Process).out
 error=$(curdir)/bam2bigwig-$(Process).out
 
 CURDIR=$(curdir)
-ANALYSIS_NAME=$$($(analysis_name):Analysis)
+ANALYSIS_NAME=$(analysis_name:Analysis)
 
 GENOME_NAME=$(GENOME_NAME)
 IN=$(ANALYSIS_NAME)-$(GENOME_NAME)_genome.bam
diff --git a/woldrnaseq/qc-coverage.condor b/woldrnaseq/qc-coverage.condor
index 9d7a02e..abc5dad 100644
--- a/woldrnaseq/qc-coverage.condor
+++ b/woldrnaseq/qc-coverage.condor
@@ -4,10 +4,10 @@ log=coverage-$(Process).log
 output=coverage-$(Process).out
 error=coverage-$(Process).out
 
-ANALYSIS_NAME=$$($(analysis_name):Analysis)
-GEORGI_DIR=$$($(georgi_dir):/woldlab/castor/home/diane/proj/GeorgiScripts)
+ANALYSIS_NAME=$(analysis_name:Analysis)
+GEORGI_DIR=$(georgi_dir:/woldlab/castor/home/diane/proj/GeorgiScripts)
 GENE_COVERAGE=$(GEORGI_DIR)/gene_coverage_wig_gtf.py
-GENOME_ROOT=$$($(genome_root):/home/diane/proj/genome/)
+GENOME_ROOT=$(genome_root:/home/diane/proj/genome/)
 GENOME_NAME=$(GENOME_NAME)
 GENOME_DIR=$(GENOME_ROOT)$(GENOME_NAME)/
 GTF=$(gtf)
diff --git a/woldrnaseq/qc-distribution.condor b/woldrnaseq/qc-distribution.condor
index b30c570..80e88a1 100644
--- a/woldrnaseq/qc-distribution.condor
+++ b/woldrnaseq/qc-distribution.condor
@@ -4,10 +4,10 @@ log=distribution-$(Process).log
 output=distribution-$(Process).out
 error=distribution-$(Process).out
 
-ANALYSIS_NAME=$$($(analysis_name):Analysis)
-GEORGI_DIR=$$($(georgi_dir):~/proj/GeorgiScripts)
+ANALYSIS_NAME=$(analysis_name:Analysis)
+GEORGI_DIR=$(georgi_dir:~/proj/GeorgiScripts)
 DISTRIBUTION=$(GEORGI_DIR)/SAM_reads_in_genes3_BAM.py
-GENOME_ROOT=$$($(genome_root):~/proj/genome/)
+GENOME_ROOT=$(genome_root:~/proj/genome/)
 GENOME_NAME=$(GENOME_NAME)
 GENOME_DIR=$(GENOME_ROOT)/$(GENOME_NAME)/
 GTF=$(gtf)
diff --git a/woldrnaseq/qc-flagstat.condor b/woldrnaseq/qc-flagstat.condor
index 4bbb198..e4d9cb2 100644
--- a/woldrnaseq/qc-flagstat.condor
+++ b/woldrnaseq/qc-flagstat.condor
@@ -1,7 +1,7 @@
 universe=vanilla
 
-#ANALYSIS_NAME=$$($(analysis_name):Analysis)
-#GENOME_ROOT=$$($(genome_root):~/proj/genome/)
+#ANALYSIS_NAME=$(analysis_name:Analysis)
+#GENOME_ROOT=$(genome_root:~/proj/genome/)
 #GENOME_NAME=$(GENOME_NAME)
 #GENOME_DIR=$(GENOME_ROOT)$(GENOME_NAME)/
 #IN=$(ANALYSIS_NAME)-$(GENOME_NAME)_genome.bam
diff --git a/woldrnaseq/qc-samstats.condor b/woldrnaseq/qc-samstats.condor
index c1f3cf9..13d47d4 100644
--- a/woldrnaseq/qc-samstats.condor
+++ b/woldrnaseq/qc-samstats.condor
@@ -4,14 +4,14 @@ log=samstats-$(Process).log
 output=samstats-$(Process).out
 error=samstats-$(Process).out
 
-ANALYSIS_NAME=$$($(analysis_name):Analysis)
-GENOME_ROOT=$$($(genome_root):~/proj/genome/)
+ANALYSIS_NAME=$(analysis_name:Analysis)
+GENOME_ROOT=$(genome_root:~/proj/genome/)
 GENOME_NAME=$(GENOME_NAME)
 GENOME_DIR=$(GENOME_ROOT)/$(GENOME_NAME)/
 CHROM_INFO=$(GENOME_DIR)chrNameLength.txt
 IN=$(ANALYSIS_NAME)-$(GENOME_NAME)_genome.bam
 OUT=$(ANALYSIS_NAME)-$(GENOME_NAME)_genome.samstats
-GEORGI_DIR=$$($(georgi_dir):~/proj/GeorgiScripts/)
+GEORGI_DIR=$(georgi_dir:~/proj/GeorgiScripts/)
 SAMSTATS=$(GEORGI_DIR)SAMstats.py
 
 request_cpus=1
diff --git a/woldrnaseq/quant-rsem.condor b/woldrnaseq/quant-rsem.condor
index f3c30d0..d324dde 100644
--- a/woldrnaseq/quant-rsem.condor
+++ b/woldrnaseq/quant-rsem.condor
@@ -4,8 +4,8 @@ output=rsem-$(Process).out
 error=rsem-$(Process).out
 environment="PATH=/usr/local/bin:/usr/bin:/bin"
 
-ANALYSIS_NAME=$$($(analysis_name):Analysis)
-GENOME_ROOT=$$($(genome_root):~/proj/genome/)
+ANALYSIS_NAME=$(analysis_name:Analysis)
+GENOME_ROOT=$(genome_root:~/proj/genome/)
 GENOME_NAME=$(GENOME_NAME)
 GENOME_DIR=$(GENOME_ROOT)/$(GENOME_NAME)/rsem
 PAIRED_END=$(paired_end)
diff --git a/woldrnaseq/rrna-premap.condor b/woldrnaseq/rrna-premap.condor
index fedaddd..811a849 100644
--- a/woldrnaseq/rrna-premap.condor
+++ b/woldrnaseq/rrna-premap.condor
@@ -3,7 +3,7 @@ log=$(CURDIR)/rrna-premap.log
 output=$(CURDIR)/rrna-premap.out
 error=$(CURDIR)/rrna-premap.out
 
-GENOME_ROOT=$$($(genome_root):/woldlab/castor/home/diane/proj/genome)
+GENOME_ROOT=$(genome_root:/woldlab/castor/home/diane/proj/genome)
 GENOME_NAME=$(GENOME_NAME)
 
 executable=$(rrna_premap_sh)
diff --git a/woldrnaseq/sort-samtools.condor b/woldrnaseq/sort-samtools.condor
index da8ec81..ec5207c 100644
--- a/woldrnaseq/sort-samtools.condor
+++ b/woldrnaseq/sort-samtools.condor
@@ -5,7 +5,7 @@ output=sort-samtools-$(Process).out
 error=sort-samtools-$(Process).out
 environment="PATH=/usr/bin:/bin"
 
-IN=$$($(in):Aligned.toTranscriptome.out.bam)
+IN=$(in:Aligned.toTranscriptome.out.bam)
 GENOME_NAME=$(GENOME_NAME)
 OUT=$(ANALYSIS_NAME)-$(GENOME_NAME)_anno.bam