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| author | Munyoki Kilyungi | 2025-07-21 23:09:11 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2025-07-22 10:15:52 +0300 |
| commit | 6fe38bd180b9041bacbb8e7b965086df590a0d45 (patch) | |
| tree | a75c5f666cc035daa4e81e26fe485ee826021495 | |
| parent | 0493bf3b1c264bb3d4bbe427d3927c836d6799e0 (diff) | |
| download | gn-machines-6fe38bd180b9041bacbb8e7b965086df590a0d45.tar.gz | |
Set path for lmdb.
We currently use lmdb for storing genotype files.
| -rwxr-xr-x | genenetwork-development-deploy.sh | 1 | ||||
| -rw-r--r-- | genenetwork-development.scm | 9 |
2 files changed, 9 insertions, 1 deletions
diff --git a/genenetwork-development-deploy.sh b/genenetwork-development-deploy.sh index b251033..d63dcf0 100755 --- a/genenetwork-development-deploy.sh +++ b/genenetwork-development-deploy.sh @@ -42,6 +42,7 @@ container_script=$(guix system container --network \ --expose=/export/data/genenetwork \ --share=/export/data/genenetwork-xapian \ --share=/export/data/genenetwork-sqlite \ + --share=/export/data/lmdb \ --share=/var/run/mysqld=/run/mysqld \ --share=/export/data/gn-docs/ \ genenetwork-development.scm) diff --git a/genenetwork-development.scm b/genenetwork-development.scm index 5b8f138..4912d11 100644 --- a/genenetwork-development.scm +++ b/genenetwork-development.scm @@ -150,6 +150,8 @@ be imported into G-expressions." (default "/export/data/genenetwork-sqlite/auth.db")) (llm-db-path genenetwork-llm-db-path (default "/export/data/genenetwork-sqlite/llm.db")) + (lmdb-data-path genenetwork-lmdb-data-path + (default "/export/data/lmdb")) (gn-guile-port genenetwork-configuration-gn-guile-port (default 8091)) (gn-doc-git-checkout genenetwork-configuration-gn-doc-git-checkout @@ -525,7 +527,7 @@ server described by CONFIG, a <genenetwork-configuration> object." "Return a G-expression that runs the latest genenetwork3 development server described by CONFIG, a <genenetwork-configuration> object." (match-record config <genenetwork-configuration> - (gn3-repository gn3-port gn3-secrets sparql-endpoint data-directory xapian-db-path auth-db-path llm-db-path) + (gn3-repository gn3-port gn3-secrets sparql-endpoint data-directory xapian-db-path auth-db-path llm-db-path lmdb-data-path) (with-manifest (package->development-manifest genenetwork3) (with-packages (list git-minimal nss-certs) (with-imported-modules '((guix build utils)) @@ -557,6 +559,7 @@ server described by CONFIG, a <genenetwork-configuration> object." #$(mixed-text-file "gn3.conf" "SPARQL_ENDPOINT=\"" sparql-endpoint "\"\n" "DATA_DIR=\"" data-directory "\"\n" + "LMDB_DATA_PATH=\"" lmdb-data-path "\"\n" "AUTH_SERVER_URL=\"https://auth-cd.genenetwork.org/\"\n" "XAPIAN_DB_PATH=\"" xapian-db-path "\"\n" "AUTH_DB=\"" auth-db-path "\"\n" @@ -775,6 +778,10 @@ described by CONFIG, a <genenetwork-configuration> object." (source "/run/mysqld") (target source) (writable? #t)) + (file-system-mapping + (source lmdb-data-path) + (target source) + (writable? #t)) ;; XXXX: FIXME: R/Qtl generates ;; files in "/tmp" and ;; "/tmp/gn2". These files are |