diff options
| -rw-r--r-- | gn/packages/genenetwork.scm | 36 | ||||
| -rw-r--r-- | gn/services/genenetwork.scm | 7 |
2 files changed, 26 insertions, 17 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index c730666..369b1ab 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -21,6 +21,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages graphviz) #:use-module (gnu packages python) #:use-module (gnu packages python-check) #:use-module (gnu packages python-crypto) @@ -35,7 +36,6 @@ #:use-module (gnu packages web) #:use-module (gnu packages wget) #:use-module (gnu packages xml) - #:use-module (past packages graphviz) #:use-module (past packages python) #:use-module (gn packages bioinformatics) #:use-module (gn packages twint) @@ -740,7 +740,7 @@ written in C") (build-system gnu-build-system) (native-inputs `(("ghostscript" ,ghostscript) - ("graphviz" ,graphviz-2.26) + ("graphviz" ,graphviz) ("python24" ,python-2.4) ("python-piddle" ,python24-piddle) ("wget" ,wget))) @@ -770,8 +770,7 @@ written in C") (substitute* '("web/webqtl/maintainance/addRif.py" "web/webqtl/networkGraph/networkGraphPage.py" "web/webqtl/utility/svg.py") - (("/usr/bin/python") (which "python")) - (("/usr/bin/env python") (which "python"))) + (("/usr/bin/(env )?python") (which "python"))) (substitute* "web/webqtl/base/webqtlConfigLocal.py" (("PythonPath.*") (string-append "PythonPath = '" (which "python") "'\n")) @@ -782,23 +781,34 @@ written in C") (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (substitute* "web/webqtl/base/webqtlConfigLocal.py" - ;; Where GN1 is located: + ;; Where GN1 is located: (GNROOT) (("/gnshare/gn") out) - ;; Where the database is located: + ;; Where the database is located: (sql_host) (("tux01") "localhost")) - ;(("tux01.uthsc.edu") "lily.uthsc.edu")) - ;; This directory is expected to be writable. + (substitute* '("web/webqtl/maintainance/QTL_Reaper_cal_lrs.py") + (("128\\.169\\.5\\.59") "localhost")) + ;; This directory (TMPDIR) is expected to be writable by apache. ;; /tmp is private inside the container. (symlink "/tmp" "web/tmp") - ;; We mount the genotypes folder in the OS-config and - ;; provide the symlink to that point in the package. + ;; IMGDIR is expected to be writable. + (symlink "/tmp" "web/image") + (system "chmod 0777 web/tmp") + ;; More writable locations: + (substitute* (list "web/webqtl/collection/ExportSelectionDetailInfoPage.py" + "web/webqtl/pairScan/DirectPlotPage.py" + "web/webqtl/updateTrait/DataUpdatePage.py" + "web/webqtl/utility/Plot.py") + (("/gnshare/gn/web/debug_file.txt") "/tmp/debug_file.txt")) + ;; We mount the genotypes folder (GENODIR) in the OS-config and + ;; provide the symlink to that location from the package. ;; And now the directory is magically available! (symlink "/gnshare/gn/web/genotypes" "web/genotypes") + (substitute* "web/webqtl/base/webqtlConfig.py" + (("http://www.genenetwork.org") "http://gn1-test.genenetwork.org")) #t))) (add-after 'unpack 'use-local-links (lambda _ (substitute* '("web/javascript/menu_items.js" - "web/webqtl/base/webqtlConfig.py" "web/webqtl/maintainance/updateMenuJS.py") (("http://(www|gn1).genenetwork.org") "")) @@ -823,10 +833,6 @@ written in C") (find-files "web/dbdoc" "\\.html")) (("src=\\\"http://www.genenetwork.org") "src=\"")) #t)) - (add-before 'install 'replace-htaccess-file - (lambda _ - (delete-file "web/webqtl/.htaccess") - #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (copy-recursively "." (assoc-ref outputs "out")) diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm index d72590d..74723ca 100644 --- a/gn/services/genenetwork.scm +++ b/gn/services/genenetwork.scm @@ -88,13 +88,16 @@ python24-svg-GN1 %base-packages)) - (services (list (service httpd-service-type + (services (list (service special-files-service-type + ;; The genotypes folder doesn't have it's shebangs patched. + `(("/usr/bin/python" ,(file-append python-2.4 "/bin/python")))) + (service httpd-service-type (httpd-configuration ;; Must be a httpd-2.2 variant. (package httpd22-with-mod-python) (config (httpd-config-file - (server-name "www.genenetwork.org") + (server-name "gn1-test.genenetwork.org") ;; Defaults to httpd, should be same as 'package' above. (server-root httpd22-with-mod-python) (user "nobody") |