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IPVC-2344: Update SeqRepo load to discover local fasta files #26

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merged 3 commits into from
Apr 25, 2024
Merged

IPVC-2344: Update SeqRepo load to discover local fasta files #26

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1dba944
feat(IPVC-2344): add tabix to be installed in Dockerfile, use environ…
bsgiles73 Apr 19, 2024
9cf17b6
feat(IPVC-2344): update seqrepo-load script to find fasta files inste…
bsgiles73 Apr 19, 2024
9120128
feat(IPVC-2344): after discussion reverting back to cp fasta files to…
bsgiles73 Apr 24, 2024
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ FROM ubuntu:22.04 as uta
ARG python_version="3.10"

# list and install dependencies
ARG dependencies="python${python_version} python3-dev python3-pip rsync git postgresql-client-14"
ARG dependencies="python${python_version} python3-dev python3-pip rsync git postgresql-client-14 tabix"

RUN apt-get update && apt-get install -y $dependencies && apt-get clean

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4 changes: 2 additions & 2 deletions docker-compose.yml
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Expand Up @@ -23,7 +23,7 @@ services:
network_mode: host
seqrepo-load:
image: uta-update
command: sbin/seqrepo-load /usr/local/share/seqrepo 2024-02-20 /seqrepo-load/work /seqrepo-load/logs
command: sbin/seqrepo-load /usr/local/share/seqrepo ${UTA_ETL_OLD_SEQREPO_VERSION} /seqrepo-load/work /seqrepo-load/logs
volumes:
- ${UTA_ETL_SEQREPO_DIR}:/usr/local/share/seqrepo
- ${UTA_ETL_WORK_DIR}:/seqrepo-load/work
Expand Down Expand Up @@ -62,7 +62,7 @@ services:
network_mode: host
splign-manual:
image: uta-update
command: sbin/uta-splign-manual 2024-02-20 ${UTA_ETL_OLD_UTA_VERSION} /uta-splign-manual/input /uta-splign-manual/work /uta-splign-manual/logs
command: sbin/uta-splign-manual ${UTA_ETL_OLD_SEQREPO_VERSION} ${UTA_ETL_OLD_UTA_VERSION} /uta-splign-manual/input /uta-splign-manual/work /uta-splign-manual/logs
depends_on:
uta:
condition: service_healthy
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4 changes: 2 additions & 2 deletions sbin/seqrepo-load
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Expand Up @@ -16,6 +16,6 @@ fi
## Load SeqRepo with new sequences
seqrepo --root-directory "$seqrepo_root" \
load -n NCBI --instance-name "$seqrepo_version" \
$sequence_dir/*.fna.gz \
$sequence_dir/*.faa.gz 2>& 1 | \
"$sequence_dir"/*.fna.gz \
"$sequence_dir"/*.faa.gz 2>& 1 | \
tee "$log_dir/seqrepo-load.log"
4 changes: 1 addition & 3 deletions sbin/uta-extract
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Expand Up @@ -38,6 +38,4 @@ sbin/filter_exonset_transcripts.py --tx-info "$working_dir/txinfo.gz" --exonsets
tee "$log_dir/filter_exonset_transcripts.log"

# move fasta files into same dir
cp -f $ncbi_dir/refseq/H_sapiens/mRNA_Prot/human.*.rna.fna.gz $working_dir/
cp -f $ncbi_dir/refseq/H_sapiens/mRNA_Prot/human.*.protein.faa.gz $working_dir/
cp -f $ncbi_dir/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405*/GCF_*_genomic.fna.gz $working_dir/
find "$ncbi_dir" -type f -name "*.f[an]a.gz" -print0 | xargs -i --null cp {} "$working_dir/"
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