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authorPjotr Prins2019-09-06 02:40:12 -0500
committerPjotr Prins2019-09-06 02:40:12 -0500
commitaea8bc0de6a1fce08a0f0adbc5b2a295264ff550 (patch)
tree2c146473b836cd9074eed9252e419a7f1c0209cd /gn
parentca6c93f743475d1f7c791f16eeb6890adc50528c (diff)
downloadguix-bioinformatics-aea8bc0de6a1fce08a0f0adbc5b2a295264ff550.tar.gz
Cleaning up genenetwork2 build.
Remove pylmm and r-phewas. Added rust-qtlreaper Fixed python-setuptools warning
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/cwl.scm2
-rw-r--r--gn/packages/genenetwork.scm9
-rw-r--r--gn/packages/python.scm4
3 files changed, 8 insertions, 7 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 84251a4..dddaa8a 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -13,7 +13,7 @@
#:use-module (gnu packages serialization)
#:use-module (gnu packages time)
#:use-module (gnu packages version-control)
- #:use-module (gn packages python)
+ ; #:use-module (gn packages python)
#:use-module (guix download)
#:use-module (guix packages)
#:use-module (guix git-download)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 27eb154..46e0407 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -31,7 +31,7 @@
#:use-module (gn packages gemma)
#:use-module (gn packages javascript)
#:use-module (gn packages phewas)
- #:use-module (gn packages python)
+ #:use-module (gn packages python)
#:use-module (gn packages python24)
#:use-module (gn packages statistics))
@@ -237,7 +237,7 @@ location of a putative QTL.")
("grep" ,grep)
("r" ,r)
("r-ctl" ,r-ctl)
- ("r-phewas" ,r-phewas)
+ ; ("r-phewas" ,r-phewas)
("r-qtl" ,r-qtl)
("r-wgcna" ,r-wgcna)
("redis" ,redis)
@@ -246,7 +246,8 @@ location of a putative QTL.")
("gemma-wrapper" ,gemma-wrapper)
; ("genenetwork2-files-small" ,genenetwork2-files-small)
("plink-ng-gn" ,plink-ng-gn)
- ("pylmm-gn2" ,pylmm-gn2)
+ ; ("pylmm-gn2" ,pylmm-gn2)
+ ("rust-qtlreaper" ,rust-qtlreaper)
("nginx" ,nginx)
("python2-flask" ,python2-flask)
("gunicorn" ,gunicorn)
@@ -310,7 +311,7 @@ location of a putative QTL.")
(lambda* (#:key inputs #:allow-other-keys)
(let* (
; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2"))
- (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
+ ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
(plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
(gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index b393ebb..3c03e26 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -412,9 +412,9 @@ until a value is returned.")
(define-public python2-rserve
(package-with-python2 python-rserve))
-(define-public python-setuptools
+(define-public python-setuptools-old
(package
- (name "python-setuptools")
+ (name "python-setuptools-old")
(version "40.6.0")
(source
(origin