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authorEfraim Flashner2022-12-11 15:03:42 +0200
committerEfraim Flashner2022-12-11 15:06:07 +0200
commitddb46629ba825ff4501528cfa1de07cb077ea6d3 (patch)
tree0f4cea04347f1e810131f829dde29612055bed3c /gn
parent4a94d82150bae9ca7a9f3926125b6a1974b229d0 (diff)
downloadguix-bioinformatics-ddb46629ba825ff4501528cfa1de07cb077ea6d3.tar.gz
gn: Fix building genenetwork1
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/python24.scm63
-rw-r--r--gn/past/genenetwork1.scm17
2 files changed, 65 insertions, 15 deletions
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm
index 7450a45..381b1ef 100644
--- a/gn/packages/python24.scm
+++ b/gn/packages/python24.scm
@@ -140,7 +140,15 @@ pre-defined variants."
(name "python24-pil")
(arguments
(substitute-keyword-arguments (package-arguments python2-pil1)
- ((#:python _) python-2.4)))))
+ ((#:python _) python-2.4)
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check))))))) ; Not applicable to python-2.4
(define-public python24-piddle
(package
@@ -148,7 +156,15 @@ pre-defined variants."
(name "python24-piddle")
(arguments
(substitute-keyword-arguments (package-arguments python2-piddle-gn)
- ((#:python _) python-2.4)))
+ ((#:python _) python-2.4)
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check))))) ; Not applicable to python-2.4
(native-inputs `(("python24-setuptools" ,python24-setuptools)))
(propagated-inputs
`(("python24-pil" ,python24-pil)))))
@@ -200,13 +216,18 @@ pre-defined variants."
(modify-phases %standard-phases
(delete 'build)
(delete 'check)
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check) ; Not applicable to python-2.4
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(sitedir (string-append out "/lib/python2.4/site-packages/json/")))
(mkdir-p sitedir)
- (copy-recursively "thirdparty/json" sitedir)
- #t))))))
+ (copy-recursively "thirdparty/json" sitedir)))))))
(home-page "")
(synopsis "")
(description "")
@@ -224,13 +245,18 @@ pre-defined variants."
(modify-phases %standard-phases
(delete 'build)
(delete 'check)
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check) ; Not applicable to python-2.4
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(sitedir (string-append out "/lib/python2.4/site-packages/svg/")))
(mkdir-p sitedir)
- (copy-recursively "thirdparty/svg" sitedir)
- #t))))))
+ (copy-recursively "thirdparty/svg" sitedir)))))))
(home-page "")
(synopsis "")
(description "")
@@ -248,6 +274,12 @@ pre-defined variants."
(modify-phases %standard-phases
(delete 'build)
(delete 'check)
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check) ; Not applicable to python-2.4
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@@ -322,7 +354,13 @@ pre-defined variants."
(modify-phases %standard-phases
(add-after 'unpack 'change-directory
(lambda _
- (chdir "thirdparty/pp-1.5.7") #t)))))
+ (chdir "thirdparty/pp-1.5.7")))
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check)))) ; Not applicable to python-2.4
(home-page "")
(synopsis "")
(description "")
@@ -346,9 +384,15 @@ pre-defined variants."
`(#:python ,python-2.4
#:phases
(modify-phases %standard-phases
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check) ; Not applicable to python-2.4
(add-before 'check 'pre-check
(lambda* (#:key inputs tests? #:allow-other-keys)
- (if tests?
+ (when tests?
(begin
(mkdir-p "/tmp/mysqld")
(call-with-output-file "/tmp/my.cnf"
@@ -368,8 +412,7 @@ pre-defined variants."
(sleep 5)
(invoke "mysqladmin" "-S" "/tmp/mysqld/mysql.sock" "variables")
(invoke "mysql" "-S" "/tmp/mysqld/mysql.sock"
- "-e" "'create database mysqldb_test charset utf8;'"))
- #t))))
+ "-e" "'create database mysqldb_test charset utf8;'"))))))
#:tests? #f)) ; TODO: Run the test suite
(native-inputs
`(("mysql" ,mysql-5.0) ; Best supported version according to the README.
diff --git a/gn/past/genenetwork1.scm b/gn/past/genenetwork1.scm
index c557ee7..c629c7e 100644
--- a/gn/past/genenetwork1.scm
+++ b/gn/past/genenetwork1.scm
@@ -110,15 +110,22 @@ location of a putative QTL.")
`(#:python ,python-2.4
#:phases
(modify-phases %standard-phases
+ (replace 'add-install-to-pythonpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PYTHONPATH"
+ (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))))
+ (delete 'sanity-check) ; Not applicable to python-2.4
(add-after 'unpack 'make-max-markername-size-larger
(lambda _
(substitute* "Src/dataset.c"
- (("512") "2048"))
- #t))
+ (("512") "2048"))))
(replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- (invoke "python" "test/runtest.py"))))))
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (setenv "PYTHONPATH" (string-append (site-packages inputs outputs) ":"
+ (getenv "PYTHONPATH")))
+ (invoke "python" "test/runtest.py")))))))
(native-inputs
`(("python24-setuptools" ,python24-setuptools)))
(home-page "http://qtlreaper.sourceforge.net/")