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authorpjotrp2016-08-14 11:08:41 +0000
committerpjotrp2016-08-14 11:08:41 +0000
commit4d6de2eaf170ebcb0d64753155ceb5c818ee70d4 (patch)
tree81f5ff39ce45628b05a0811eab0d80d57929555e /gn/packages
parentb3394e07071d11674cc796e6a4a3de5fc4634a78 (diff)
downloadguix-bioinformatics-4d6de2eaf170ebcb0d64753155ceb5c818ee70d4.tar.gz
GN2: reintroducing python2-pil
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/genenetwork.scm19
-rw-r--r--gn/packages/python.scm4
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.