From 22a219367914425f8de39c93c442c81c06de95cd Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 24 Mar 2023 04:47:04 -0500
Subject: Instructions for running in a container and added dependencies

---
 .gitignore   |  2 +-
 README.md    | 12 ++++++++++++
 conn.scm     | 12 ++++++++++++
 manifest.scm |  6 +++---
 4 files changed, 28 insertions(+), 4 deletions(-)
 create mode 100644 conn.scm

diff --git a/.gitignore b/.gitignore
index 472fecd..e796b66 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1 @@
-*.go
\ No newline at end of file
+*.go
diff --git a/README.md b/README.md
index 57deb52..0de0eed 100644
--- a/README.md
+++ b/README.md
@@ -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))
-- 
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