diff options
| author | Pjotr Prins | 2023-03-24 04:47:04 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2023-03-24 04:47:04 -0500 |
| commit | 22a219367914425f8de39c93c442c81c06de95cd (patch) | |
| tree | 120892bf36f0258bed93c20cdea73671299429dd | |
| parent | d31b9f5dac6d35b3a60eafbed4911446e8f89c61 (diff) | |
| download | gn-transform-databases-22a219367914425f8de39c93c442c81c06de95cd.tar.gz | |
Instructions for running in a container and added dependencies
| -rw-r--r-- | .gitignore | 2 | ||||
| -rw-r--r-- | README.md | 12 | ||||
| -rw-r--r-- | conn.scm | 12 | ||||
| -rw-r--r-- | manifest.scm | 6 |
4 files changed, 28 insertions, 4 deletions
@@ -1 +1 @@ -*.go
\ No newline at end of file +*.go @@ -21,6 +21,18 @@ Build the sources. $ make ``` +or for a container + +```shell +guix shell -C --network --share=/run/mysqld/ +make +export GUILE_LOAD_PATH=.:$GUILE_LOAD_PATH +mkdir test +echo "Dumping databases..." +guile ./dump.scm conn.scm test/ +``` + + ## Set up connection parameters Describe the database connection parameters in a file *conn.scm* file as diff --git a/conn.scm b/conn.scm new file mode 100644 index 0000000..8a552ab --- /dev/null +++ b/conn.scm @@ -0,0 +1,12 @@ +((sql-username . "webqtlout") + (sql-password . "webqtlout") + (sql-database . "db_webqtl") + (sql-host . "localhost") + (sql-port . 3306) + (virtuoso-port . 8891) + (virtuoso-username . "dba") + (virtuoso-password . "dba") + (sparql-scheme . http) + (sparql-host . "localhost") + (sparql-port . 8892) + (generif-data-file . "/export3/local/home/bonfacem/dump-genenetwork-database/generifs_basic.gz")) diff --git a/manifest.scm b/manifest.scm index ac4026e..6e08f09 100644 --- a/manifest.scm +++ b/manifest.scm @@ -7,7 +7,7 @@ (use-modules (gnu packages autotools) ((gnu packages base) #:select (gnu-make)) ((gnu packages bioinformatics) #:prefix guix:) - ((gnu packages databases) #:select (virtuoso-ose)) + ((gnu packages databases) #:select (virtuoso-ose mariadb)) (gnu packages graphviz) (gnu packages guile) ((gnu packages guile-xyz) #:select (guile-sparql) #:prefix guix:) @@ -71,8 +71,8 @@ (license license:gpl3+))) (packages->manifest - (list gnu-make guile-3.0 guile-dbi guile-dbd-mysql + (list gnu-make guile-3.0 guile-dbi guile-dbd-mysql guile-zlib ;; We abuse (ccwl graphviz) as a library to visualize the database ;; schema. Hence we need ccwl and guile-libyaml. ccwl graphviz guile-hashing guile-libyaml guile-sparql - raptor2 run64 virtuoso-ose)) + raptor2 run64 virtuoso-ose mariadb)) |