More updates #33
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| Original file line number | Diff line number | Diff line change |
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| #!/bin/bash | ||
| #SBATCH --job-name=human_download | ||
| #SBATCH --time=1-0 | ||
| #SBATCH --ntasks=1 | ||
| #SBATCH --cpus-per-task=1 | ||
| #SBATCH --mem=32G | ||
| #SBATCH -o %x-%j.out | ||
| #SBATCH -e %x-%j.err | ||
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| DEST=/scratch/$PAWSEY_PROJECT/$USER/Databases/human | ||
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| mkdir -p $DEST | ||
| cd $DEST | ||
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| if [[ -e GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz ]]; then | ||
| echo "GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz already exists. Nothing to do"; | ||
| touch GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz; | ||
| exit 0 | ||
| fi | ||
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| curl -LO https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz | ||
| echo "Downloaded human db to $DEST" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| #!/bin/bash | ||
| #SBATCH --job-name=taxon_dld | ||
| #SBATCH --time=1-0 | ||
| #SBATCH --ntasks=1 | ||
| #SBATCH --cpus-per-task=1 | ||
| #SBATCH --mem=32G | ||
| #SBATCH -o %x-%j.out | ||
| #SBATCH -e %x-%j.err | ||
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| TAXDIR="/scratch/$PAWSEY_PROJECT/$USER/Databases/NCBI/taxonomy/current" | ||
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| mkdir -p $TAXDIR | ||
| cd $TAXDIR; | ||
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| required_files=( | ||
| citations.dmp delnodes.dmp division.dmp gc.prt | ||
| gencode.dmp images.dmp merged.dmp names.dmp | ||
| nodes.dmp readme.txt | ||
| ) | ||
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| missing=0 | ||
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| for file in "${required_files[@]}"; do | ||
| if [[ ! -f "$file" ]]; then | ||
| echo "Missing: $file" | ||
| missing=1 | ||
| fi | ||
| done | ||
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| if [[ $missing -eq 1 ]]; then | ||
| echo "One or more files are missing. Downloading taxdump.tar.gz..." | ||
| curl -LO https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz | ||
| tar zxf taxdump.tar.gz && rm -f taxdump.tar.gz | ||
|
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If the taxonomy transfer is interrupted or the archive is corrupt, Useful? React with 👍 / 👎. There was a problem hiding this comment. Summary
Testing
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| else | ||
| echo "All required files are present." | ||
| fi | ||
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| echo "Done" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| #!/bin/bash | ||
| #SBATCH --job-name=MMSeqsDld100 | ||
| #SBATCH --time=1-0 | ||
| #SBATCH --ntasks=1 | ||
| #SBATCH --cpus-per-task=1 | ||
| #SBATCH --mem=128G | ||
| #SBATCH -o %x-%j.out | ||
| #SBATCH -e %x-%j.err | ||
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| # Use `mmseqs databases` to find information about the preformatted databases | ||
| # NOTE: Do not download the NT database unless you _really_ need it. The database is huge! | ||
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| set -euo pipefail | ||
| trap 's=$?; echo "$0: Error on line "$LINENO": $BASH_COMMAND"; exit $s' ERR | ||
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| # test we have atavide_lite conda installed, and then activate it | ||
| eval "$(conda shell.bash hook)" | ||
| "$HOME/GitHubs/atavide_lite/pawsey_lib/check_atavide_lite_env.sh" | ||
| ATAVIDE_CONDA="/scratch/$PAWSEY_PROJECT/$USER/software/miniconda3/atavide_lite" | ||
| conda activate $ATAVIDE_CONDA | ||
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| CWD=`pwd` | ||
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| #DB can also be UniRef100 UniRef100 GTDB etc | ||
| DB=UniRef100 | ||
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| required_files=( | ||
| UniRef100 UniRef100.dbtype UniRef100_h UniRef100_h.dbtype | ||
| UniRef100_h.index UniRef100.index UniRef100.lookup UniRef100_mapping | ||
| UniRef100.source UniRef100_taxonomy UniRef100.version | ||
| ) | ||
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| missing=0 | ||
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| DESTINATION=/scratch/$PAWSEY_PROJECT/$USER/Databases/$DB | ||
| TMP=/scratch/$PAWSEY_PROJECT/$USER/tmp | ||
| mkdir -p $DESTINATION $TMP | ||
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| cd $DESTINATION | ||
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| for file in "${required_files[@]}"; do | ||
| if [[ ! -f "$DB/$file" ]]; then | ||
| echo "Missing: $DB/$file" | ||
| missing=1 | ||
| fi | ||
| done | ||
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| if [[ $missing -eq 0 ]]; then | ||
| echo "All required files are present." | ||
| exit 0 | ||
| fi | ||
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| echo "Downloading required files" | ||
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| cd $CWD | ||
| # delete the old Destination and make the dir to remove partial files. | ||
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| rm -rf $DESTINATION && mkdir -p $DESTINATION | ||
| TPD=$(mktemp -d -p $TMP) | ||
| echo -e "Downloading to $DESTINATION/$DB and using temp location $TPD.\nNote we download the tarball and then uncompress, so there is usually nothing in the output for a while!" >&2 | ||
| mmseqs databases --threads 8 $DB $DESTINATION/$DB $TPD | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| #!/bin/bash | ||
| #SBATCH --job-name=MMSeqsDld | ||
| #SBATCH --time=1-0 | ||
| #SBATCH --ntasks=1 | ||
| #SBATCH --cpus-per-task=1 | ||
| #SBATCH --mem=128G | ||
| #SBATCH -o %x-%j.out | ||
| #SBATCH -e %x-%j.err | ||
|
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||
| # Use `mmseqs databases` to find information about the preformatted databases | ||
| # NOTE: Do not download the NT database unless you _really_ need it. The database is huge! | ||
|
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| set -euo pipefail | ||
| trap 's=$?; echo "$0: Error on line "$LINENO": $BASH_COMMAND"; exit $s' ERR | ||
|
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||
| # test we have atavide_lite conda installed, and then activate it | ||
| eval "$(conda shell.bash hook)" | ||
| "$HOME/GitHubs/atavide_lite/pawsey_lib/check_atavide_lite_env.sh" | ||
| ATAVIDE_CONDA="/scratch/$PAWSEY_PROJECT/$USER/software/miniconda3/atavide_lite" | ||
| conda activate $ATAVIDE_CONDA | ||
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| CWD=`pwd` | ||
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| #DB can also be UniRef50 UniRef100 GTDB etc | ||
| DB=UniRef50 | ||
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| required_files=( | ||
| UniRef50 UniRef50.dbtype UniRef50_h UniRef50_h.dbtype | ||
| UniRef50_h.index UniRef50.index UniRef50.lookup UniRef50_mapping | ||
| UniRef50.source UniRef50_taxonomy UniRef50.version | ||
| ) | ||
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| missing=0 | ||
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| DESTINATION=/scratch/$PAWSEY_PROJECT/$USER/Databases/$DB | ||
| TMP=/scratch/$PAWSEY_PROJECT/$USER/tmp | ||
| mkdir -p $DESTINATION $TMP | ||
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| cd $DESTINATION | ||
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| for file in "${required_files[@]}"; do | ||
| if [[ ! -f "$DB/$file" ]]; then | ||
| echo "Missing: $DB/$file" | ||
| missing=1 | ||
| fi | ||
| done | ||
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| if [[ $missing -eq 0 ]]; then | ||
| echo "All required files are present." | ||
| exit 0 | ||
| fi | ||
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| echo "Downloading required files" | ||
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| cd $CWD | ||
| # delete the old Destination and make the dir to remove partial files. | ||
|
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| rm -rf $DESTINATION && mkdir -p $DESTINATION | ||
| TPD=$(mktemp -d -p $TMP) | ||
| echo -e "Downloading to $DESTINATION/$DB and using temp location $TPD.\nNote we download the tarball and then uncompress, so there is usually nothing in the output for a while!" >&2 | ||
| mmseqs databases --threads 8 $DB $DESTINATION/$DB $TPD | ||
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If this transfer is interrupted or receives an HTTP error, the script has neither
set -enor curl's--failbehavior (curl documentation), so it proceeds to the finalechoand reports a successful Slurm job. Because-Owrites directly to the final filename and the earlier guard checks only existence, a partial or error-response file is then accepted as a complete human database on every retry; propagate curl failures and download atomically before exposing the final filename.Useful? React with 👍 / 👎.