diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 19 | ||||
| -rw-r--r-- | gn/packages/python.scm | 4 |
2 files changed, 11 insertions, 12 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 10f0a26..81873d5 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -98,13 +98,13 @@ (url "https://github.com/genenetwork/genenetwork.git") ;; (url "https://github.com/pjotrp/genenetwork.git") (commit commit))) - (file-name (string-append name "-" commit)) + (file-name (string-append name "-" commit)) (sha256 (base32 "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py")))) (propagated-inputs `( ("python" ,python-2) ;; probably superfluous - ("r" ,r) + ("r" ,r) )) (inputs `( ;; http://spring211.uthsc.edu/gn/thirdparty.tbz @@ -125,7 +125,7 @@ ; ("python2-simplejson" ,python2-simplejson) ; ("python2-pyyaml" ,python2-pyyaml) ;; python-yolk is not needed - ("python2-pillow" ,python2-pillow) + ("python2-pil" ,python2-pil) ("python2-numarray" ,python2-numarray) ("plink" ,plink) ;; gn1 ; ("r-qtl" ,r-qtl) @@ -181,14 +181,14 @@ ("python2-passlib" ,python2-passlib) ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) - ("python2-pillow" ,python2-pillow) + ("python2-pil" ,python2-pil) ; should move to pillow some day ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) ("python2-scipy" ,python2-scipy) ("python2-simplejson" ,python2-simplejson) ("python2-pyyaml" ,python2-pyyaml) ("python2-xlsxwriter" ,python2-xlsxwriter) - ("qtlreaper" ,qtlreaper) + ("qtlreaper" ,qtlreaper) )) (build-system python-build-system) (arguments @@ -203,7 +203,7 @@ ;; (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2")) (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) ) - + (substitute* '("etc/default_settings.py") (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) @@ -229,7 +229,7 @@ (origin (method url-fetch) (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") - (file-name (string-append name "-" pfff)) + (file-name (string-append name "-" pfff)) (sha256 (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) (build-system trivial-build-system) @@ -251,7 +251,7 @@ (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) ) - (and + (and (zero? (system* lz4unpack source "-d" tarfn)) (zero? (system* tar "xf" tarfn)) (mkdir-p targetdir) @@ -271,7 +271,7 @@ (origin (method url-fetch) (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip") - (file-name (string-append name "-" md5)) + (file-name (string-append name "-" md5)) (sha256 (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x")))) (build-system trivial-build-system) @@ -292,4 +292,3 @@ (synopsis "Small database to run on genenetwork") (description "Genenetwork installation + database.") (license license:agpl3+)))) - diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 1d071fa..3462978 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -308,7 +308,7 @@ version "-gn.tar.gz")) (install-file "ImageH.pyc" lib) (install-file "ImagePaletteH.pyc" lib) (install-file "__init__.pyc" lib) - ))) ; install + ))) ; install ) ; phases #:tests? #f)) (home-page @@ -343,7 +343,7 @@ project)") `(("freetype" ,freetype) ("libjpeg" ,libjpeg) ("libtiff" ,libtiff) - ("python-setuptools" ,python-setuptools) + ("python2-setuptools" ,python2-setuptools) ("zlib" ,zlib))) (arguments ;; Only the fork python-pillow works with Python 3. |