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Makefile
42 lines (28 loc) · 1.53 KB
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Makefile
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getgenome:
cd input; wget ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
getuniprot:
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000000589_10090.fasta.gz
#scp UP000000589_10090.fasta.gz beagle.henlab.org:/data/henlab/ref_genome/mouse/uniprot.fa.gz to /homology/uniprot.fa
put_red_uniprot:
#the renamed uniprot file for BLASTing
#scp uniprot.red.fa beagle.henlab.org:/data/henlab/ref_genome/mouse/uniprot.fa
get_blastp:
#scp beagle.henlab.org:/data/henlab/ref_genome/mouse/results_prot.out.gz ./mouse_all2lall_blast_prot.csv.gz
make_blastdb:
makeblastdb -in uniprot.fa -title "mouse_protein" -dbtype prot
runblast:
blastp -db uniprot.fa -query uniprot.fa -out results_prot.out -outfmt 6
mount:
sshfs beagle.henlab.org:/data/henlab/project/bias/new/greta ./x
uploadfeature:
scp greta/feature/* beagle.henlab.org:/data/henlab/project/bias/new/greta/feature/
#scp totfeature.csv beagle.henlab.org:/data/henlab/project/bias/new/
#scp features/* beagle.henlab.org:/data/henlab/project/bias/new/features/
downloadfeature:
scp beagle.henlab.org:/data/henlab/project/bias/new/features/* feature/
scp beagle.henlab.org:/data/henlab/project/bias/new/totfeature.csv ./
uploadwebsite:
scp website/data/*sqlite beagle.henlab.org:/data/henlab/project/bias/new/website/data/
getgreta:
scp -r beagle.henlab.org:/data/henlab/project/bias/new/greta/feature greta/
scp -r beagle.henlab.org:/data/henlab/project/bias/new/greta/out greta/