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| author | Pjotr Prins | 2024-01-01 17:47:34 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2024-01-01 17:47:34 +0100 |
| commit | 691eed969ac4bb9fa43358b9a8e0d1ea43accbea (patch) | |
| tree | 69a38708a10b8f525b465332796e636aac9d52e6 /scripts/precompute | |
| parent | 0799806735942cc3d44626c3c8b54402343a47f5 (diff) | |
| download | gn-guile-691eed969ac4bb9fa43358b9a8e0d1ea43accbea.tar.gz | |
Run gemma-wrapper with metadata
Diffstat (limited to 'scripts/precompute')
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 11 |
1 files changed, 5 insertions, 6 deletions
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 8588061..2036adc 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -1,10 +1,10 @@ #! Run from base dir with -.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm +. .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm and with some extra paths -.guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- guile -L . -s ./scripts/precompute/precompute-hits.scm +. .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/precompute-hits.scm You may want to forward a mysql port if there is no DB locally @@ -25,7 +25,6 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org ) - ;; potentially you want to test connection with mysql client: ;; ;; mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;" @@ -59,8 +58,8 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org ;; ---- get first available dataset for precompute: ;; @@ order by dataid - recurse - (define (get-trait-name db probeset-id) - (dbi-query db (string-append "select Name,Symbol from ProbeSet where Id=" (int-to-string probeset-id) " limit 1")) + (define (get-trait db probeset-id) + (dbi-query db (string-append "select Id,Chr,Mb,Name,Symbol,description from ProbeSet where Id=" (int-to-string probeset-id) " limit 1")) (get-row db) ) @@ -70,7 +69,7 @@ ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org (data-id-str (int-to-string data-id)) (probesetfreeze-id (assoc-ref hit "ProbeSetFreezeId")) (probeset-id (assoc-ref hit "ProbeSetId")) - (trait (get-trait-name db probeset-id)) + (trait (get-trait db probeset-id)) (trait-name (assoc-ref trait "Name")) (name (dataset-name db probesetfreeze-id)) ] |