Commit 4ad913ba authored by Holger Brandl's avatar Holger Brandl

fixed custom mouse igenome build

parent f74a8f8c
......@@ -46,10 +46,10 @@ samtools faidx genome.fa &
mcdir ${IGENOME_BASE}/Annotation
mcdir ${IGENOME_BASE}/Annotation/Genes
wget ftp://ftp.ensembl.org/pub/release-88/gtf/homo_sapiens/Homo_sapiens.GRCh38.88.gtf.gz
#wget ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/Mus_musculus.GRCm38.92.gtf.gz
#wget ftp://ftp.ensembl.org/pub/release-88/gtf/homo_sapiens/Homo_sapiens.GRCh38.88.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/Mus_musculus.GRCm38.92.gtf.gz
gunzip -c Homo_sapiens.GRCh38.88.gtf.gz > genes.gtf
gunzip -c Mus_musculus.GRCm38.92.gtf.gz > genes.gtf
#head genes.gtf
ll ${IGENOME_BASE}/Sequence/WholeGenomeFasta/genome.fa
......@@ -75,4 +75,6 @@ jl submit "kallisto index -i ${refFasta}.kallisto.idx ${refFasta}"
jl wait --email
wait # for star index creation
mailme "igenome build done in $(pwd)"
\ No newline at end of file
mailme "igenome build done in $(pwd)"
chmod -R u-w ${IGENOME_BASE}
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