Skip to content

Update parameters to build the suffix-array so we can also use the mmap option #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
tibvdm wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Update parameters to build the suffix-array so we can also use the mmap option #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
cfd4137
Updated script (still contains reference to other branch)
tibvdm Mar 17, 2026
95b95e6
remove dependency
tibvdm Mar 30, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
.idea
*.iml
**/node_modules/
/data
/home
9 changes: 4 additions & 5 deletions scripts/update-uniprot/update_uniprot.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -201,7 +201,7 @@ generate_tables() {
log "Started building and generating Unipept table files."

# Start the download and generation of all the suffix array tables
"/${SCRATCH_DIR:?}/unipept-database/scripts/generate_sa_tables.sh" --database-sources "$DATABASE_SOURCES" --output-dir "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/tables" --temp-dir "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/temp"
"${SCRATCH_DIR:?}/unipept-database/scripts/generate_sa_tables.sh" --database-sources "$DATABASE_SOURCES" --output-dir "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/tables" --temp-dir "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/temp"

# Check if the required files are present and have been generated successfully
local required_files=(
Expand Down Expand Up @@ -256,7 +256,7 @@ build_suffix_array() {
rm -rf "${SCRATCH_DIR:?}/unipept-index"

# Download new version of the index repo
git clone --quiet "https://github.com/unipept/unipept-index.git" "${SCRATCH_DIR:?}/unipept-index"
git clone -b feature/speedup-loading-index --quiet "https://github.com/unipept/unipept-index.git" "${SCRATCH_DIR:?}/unipept-index"
Copy link
Copy Markdown

@SimonVandeVyver SimonVandeVyver Apr 13, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The script is still using the feature branch


Comment thread
tibvdm marked this conversation as resolved.
log "Successfully cloned unipept-index repo."

Expand All @@ -269,7 +269,7 @@ build_suffix_array() {
log "Started building suffix array"

# Start the construction of the binary suffix array file
"/${SCRATCH_DIR:?}/unipept-index/target/release/sa-builder" -a "lib-sais" -s 2 -c --database-file "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/suffix-array"/proteins.tsv --output "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/suffix-array/sa.bin"
"${SCRATCH_DIR:?}/unipept-index/target/release/sa-builder" -a "lib-sais" -s 2 -c --database-file "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/suffix-array"/proteins.tsv --output-sa "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/suffix-array/sa.bin" --output-proteins "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/suffix-array/proteins.bin" --output-mapping "${OUTPUT_DIR:?}/uniprot-${uniprot_version}/suffix-array/mapping.bin"

log "Finished building suffix array"
}
Expand Down Expand Up @@ -366,7 +366,7 @@ setup_opensearch() {

log "Start importing proteins in OpenSearch instance."

"/${SCRATCH_DIR:?}/unipept-database/scripts/initialize_opensearch.sh" --uniprot-entries "${OUTPUT_DIR}/uniprot-${uniprot_version}/tables/uniprot_entries.tsv.lz4"
"${SCRATCH_DIR:?}/unipept-database/scripts/initialize_opensearch.sh" --uniprot-entries "${OUTPUT_DIR}/uniprot-${uniprot_version}/tables/uniprot_entries.tsv.lz4"

log "Finished importing proteins in OpenSearch instance."
}
Expand Down Expand Up @@ -644,7 +644,6 @@ if [[ "$MODE" == *"update"* ]]; then
checkdep uuidgen
checkdep pv
checkdep pigz
checkdep build-essential
checkdep cmake

setup_directories "$UNIPROTKB_VERSION"
Expand Down