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authorEfraim Flashner2021-09-17 12:25:34 +0300
committerEfraim Flashner2021-09-17 12:25:34 +0300
commit0684b02dacdd6fcbb84629474744b94554b4305c (patch)
treeb8a94fa25a54fda8104a8a034cb73c8a795d6e36 /gn
parent8bd585606b67c09a91912307026a68bacc0fb1d9 (diff)
downloadguix-bioinformatics-0684b02dacdd6fcbb84629474744b94554b4305c.tar.gz
gn: Use known good binary version of direct.so for genenetwork1
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/python24.scm48
-rw-r--r--gn/past/genenetwork1.scm2
2 files changed, 49 insertions, 1 deletions
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm
index 6f550a1..35cd91e 100644
--- a/gn/packages/python24.scm
+++ b/gn/packages/python24.scm
@@ -4,6 +4,7 @@
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
+ #:use-module (guix build-system copy)
#:use-module (guix build-system python)
#:use-module (gn packages databases)
#:use-module (gn packages python)
@@ -11,6 +12,7 @@
#:use-module (past packages tls)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
+ #:use-module (gnu packages elf)
#:use-module (gnu packages gcc)
#:use-module (gnu packages maths)
#:use-module (gnu packages python-xyz)
@@ -388,6 +390,7 @@ for Python. The design goals are:
@end itemize")
(license license:gpl2+)))
+;; It seems this isn't the correct DIRECT binary
(define-public python24-direct
(package
(name "python24-direct")
@@ -457,3 +460,48 @@ algorithm can be found in Gablonsky's
@url{http://repository.lib.ncsu.edu/ir/bitstream/1840.16/3920/1/etd.pdf,
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")
+ (file-name "direct.so")
+ (sha256
+ (base32
+ "0kj11dbi25k0wvyxxsylx7dsc7wm7rja799fymklkdd8h561la4i"))))
+ (build-system copy-build-system)
+ (arguments
+ `(#:install-plan
+ '(("direct.so" "lib/python2.4/site-packages/"))
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'unpack
+ (lambda* (#:key inputs #:allow-other-keys)
+ (copy-file (assoc-ref inputs "source") "direct.so")
+ #t))
+ (add-after 'unpack 'patchelf
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Writable so we can use patchelf, executable so it is useful.
+ ;; After installation the writable bit is stripped off.
+ (chmod "direct.so" #o777)
+ (invoke "patchelf"
+ "--set-rpath"
+ (string-append (assoc-ref inputs "gcc:lib") "/lib")
+ "direct.so")
+ #t)))))
+ (inputs
+ `(("gcc:lib" ,gcc "lib")))
+ (native-inputs
+ `(("patchelf" ,patchelf)))
+ (home-page "")
+ (synopsis "")
+ (description "")
+ (license #f)))
diff --git a/gn/past/genenetwork1.scm b/gn/past/genenetwork1.scm
index b14d787..c557ee7 100644
--- a/gn/past/genenetwork1.scm
+++ b/gn/past/genenetwork1.scm
@@ -158,7 +158,7 @@ location of a putative QTL.")
(propagated-inputs
`(("python" ,python-2.4)
("httpd-with-mod-python" ,httpd22-with-mod-python)
- ("python-direct" ,python24-direct)
+ ("python-direct" ,python24-direct-gn)
("python-htmlgen-GN1" ,python24-htmlgen-GN1)
("python-json-GN1" ,python24-json-GN1)
("python-mysqlclient" ,python24-mysqlclient)