Commit 6be879ed authored by JihedC's avatar JihedC
Browse files

attempt to fix the download of gene gtf

parent 63c28e21
......@@ -16,6 +16,7 @@ WORKING_DIR = config["working_dir"]
RESULT_DIR = config["results_dir"]
DATA_DIR = config["data_dir"]
GENOME_FASTA_URL = config["genome_fasta_url"]
GENE_GTF_URL = config["gene_gtf_url"]
#units = pd.read_table(config["units"], dtype=str).set_index(["bed"], drop=False)
......
......@@ -11,6 +11,7 @@ units : "units.tsv"
## genome reference ##
genome_fasta_url : "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.primary_assembly.genome.fa.gz"
gene_gtf_url: "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz"
HMMRATAC: "https://github.com/LiuLabUB/HMMRATAC/releases/download/1.2.10/HMMRATAC_V1.2.10_exe.jar"
......@@ -55,4 +56,4 @@ bamCoverage:
# computeMatrix
ComputeMatrix:
GTF: "gencode.vM25.annotation.gtf"
GTF: "gencode.vM25.annotation.gtf"
......@@ -71,7 +71,7 @@ rule ComputeMatrix:
conda:
"envs/deeptools.yaml"
params:
GTF = str(config['ComputeMatrix']['GTF'])
GTF = WORKING_DIR + "gtf_gene.gtf"
shell:
"computeMatrix reference-point -S {input} -R {params.GTF} -o {output} -a 3000 -b 3000 2>{log}"
......
......@@ -9,6 +9,12 @@ rule download_genome:
"wget -O {output} {GENOME_FASTA_URL}"
rule download_gene_gtf:
output:
WORKING_DIR + "gtf_gene.gtf"
shell:
"curl {GENE_GTF_URL} | gunzip -c > {output}"
rule index_genome:
input:
WORKING_DIR + "reference",
......
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