chm13 rDNA to git

marbl · Jan 9, 2024 · b2b2a72 · b2b2a72
1 parent be43669
commit b2b2a72
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Showing 3 changed files with 165,478 additions and 1 deletion.
diff --git a/src/Makefile b/src/Makefile
@@ -760,6 +760,7 @@ all: $(addprefix ${TARGET_DIR}/,${ALL_TGTS}) \
      ../lib/verkko/data/human-ebv-AJ507799.2.fasta.gz \
      ../lib/verkko/data/human-mito-NC_012920.1.fasta.gz \
      ../lib/verkko/data/human-rdna-KY962518.1.fasta.gz \
+     ../lib/verkko/data/chm13_rDNAs.fa \
      \
      ../lib/verkko/scripts/add_fake_alignments.py \
      ../lib/verkko/scripts/add_fake_bridging_paths.py \

diff --git a/src/Snakefiles/8-hicPipeline.sm b/src/Snakefiles/8-hicPipeline.sm
@@ -138,7 +138,7 @@ cat > ./run_rdnamashmap.sh <<EOF
 #!/bin/sh
 set -e
 echo "---Running MashMap"
-{params.MASHMAP} -r /data/antipovd2/devel/ribotin/template_seqs/chm13_rDNAs.fa  -q ../{input.unitigs} -t {threads} --pi 95.0 -s 5000 -o ../{output.unitigs_rdnamatches}
+{params.MASHMAP} -r {VERKKO}/data/chm13_rDNAs.fa  -q ../{input.unitigs} -t {threads} --pi 95.0 -s 5000 -o ../{output.unitigs_rdnamatches}
 EOF
 
 chmod +x ./run_rdnamashmap.sh