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author | Shepherd on Tux02 | 2024-06-20 07:26:21 -0500 |
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committer | Shepherd on Tux02 | 2024-06-20 07:26:21 -0500 |
commit | f0f8dc84eca7088177797f84db05314537615c77 (patch) | |
tree | 5a7408a19c92b0c4d536916269425d883c4f06ca /gn/packages/python24.scm | |
parent | 951e77b10c84889f29c1f2322087c796cedb375a (diff) | |
parent | 48af9393cf186230e08b0fa6f7f443bc818408d2 (diff) | |
download | guix-bioinformatics-f0f8dc84eca7088177797f84db05314537615c77.tar.gz |
Merge branch 'master' of https://gitlab.com/genenetwork/guix-bioinformatics
Diffstat (limited to 'gn/packages/python24.scm')
-rw-r--r-- | gn/packages/python24.scm | 72 |
1 files changed, 55 insertions, 17 deletions
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm index 35cd91e..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))))) @@ -182,7 +198,7 @@ pre-defined variants." (define GN1-thirdparty-sources (origin (method url-fetch/tarbomb) - (uri "http://ipfs.genenetwork.org/ipfs/QmTPwYT2pehdxdG1TiHEzVzLgbeuhJ4utXShuz3twA84AB/thirdparty.tgz") + (uri "https://files.genenetwork.org/software/thirdparty.tgz") (file-name "GN1-thirdparty") (sha256 (base32 @@ -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. @@ -461,18 +504,13 @@ algorithm can be found in Gablonsky's thesis}.") (license license:expat))) -; env IPFS_PATH=/export/ipfs/ ipfs add direct.so -; added QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA direct.so -; penguin2:~/tmp$ env IPFS_PATH=/export/ipfs/ ipfs pin add QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA -; pinned QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA recursively - (define-public python24-direct-gn (package (name "python24-direct-gn") (version "GN") (source (origin (method url-fetch) - (uri "http://ipfs.genenetwork.org/ipfs/QmYUZiuAP6DJeubu69JqvRWSsn53qCZCS3FkRWgTowtWkA") + (uri "https://files.genenetwork.org/software/direct.so") (file-name "direct.so") (sha256 (base32 |