diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 151 |
1 files changed, 0 insertions, 151 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 896767b..43e61a2 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -47,45 +47,6 @@ #:use-module (gn packages statistics) #:use-module (srfi srfi-1)) -(define-public my-deploy - (package - (name "my-deploy") - (version "0.0.1") - (source #f) - (build-system trivial-build-system) - (arguments - `(#:guile ,%bootstrap-guile - #:modules ((guix build utils)) - #:builder - (let* ((out (assoc-ref %outputs "out")) - (bash (assoc-ref %build-inputs "bash")) - (foo (string-append out "/foo"))) - (begin - (use-modules (guix build utils)) - (mkdir out) - (call-with-output-file foo - (lambda (p) - (format p - "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%" - bash))) - (chmod foo #o777) - ;; wrap-program uses `which' to find bash for the wrapper - ;; shebang, but it can't know about the bootstrap bash in - ;; the store, since it's not named "bash". Help it out a - ;; bit by providing a symlink it this package's output. - (symlink bash (string-append out "/bash")) - (setenv "PATH" out) - (wrap-program foo `("GUIX_FOO" prefix ("hello"))) - (wrap-program foo `("GUIX_BAR" prefix ("world"))) - #t)))) - (inputs `(("bash" ,(search-bootstrap-binary "bash" - (%current-system))))) - - (home-page #f) - (synopsis #f) - (description #f) - (license #f))) - (define-public r-wgcna (package (name "r-wgcna") @@ -307,118 +268,6 @@ association studies (GWAS).") (license license:gpl3)))) -(define-public genenetwork1 - (let ((commit "d622c803b")) - (package - (name "genenetwork1") - (version (string-append "1.0-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/genenetwork/genenetwork.git") - ;; (url "https://github.com/pjotrp/genenetwork.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py")))) - (propagated-inputs `( - ("python" ,python-2) ;; probably superfluous - ("r" ,r) - )) - (inputs `( - ;; http://spring211.uthsc.edu/gn/thirdparty.tbz - ;; graphviz-2.22.2 htmlgen json numarray-1.5.2 piddle PIL pp-1.5.7 pyx pyXLWriter svg - ("mysql" ,mysql) - ("nginx" ,nginx) - ("graphviz" ,graphviz) - ; ("python2-jinja2" ,python2-jinja2) - ; ("python2-sqlalchemy" ,python2-sqlalchemy) - ; ("python2-setuptools" ,python2-setuptools) - ; ("python2-scipy" ,python2-scipy) - ;; looks like python-numarray is not needed - ; ("python2-numpy" ,python2-numpy) - ; ("python2-pandas" ,python2-pandas) - ; ("python2-passlib" ,python2-passlib) - ; ("python2-redis" ,python2-redis) - ; ("python2-requests" ,python2-requests) - ; ("python2-simplejson" ,python2-simplejson) - ; ("python2-pyyaml" ,python2-pyyaml) - ;; python-yolk is not needed - ("python2-pil" ,python2-pil) - ("python2-numarray" ,python2-numarray) - ("plink" ,plink) ;; gn1 - ; ("r-qtl" ,r-qtl) - )) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; no 'setup.py test' - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) - -(define-public genenetwork2 - (let ((commit "9e9475053")) - (package - (name "genenetwork2") - (version (string-append "2.0-" commit )) - (source (origin - (method git-fetch) - (uri (git-reference - ;; (url "https://github.com/genenetwork/genenetwork2.git") - (url "https://github.com/pjotrp/genenetwork2.git") - (commit commit))) - (file-name (string-append name "-" commit)) - (sha256 - (base32 - "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd")))) - (propagated-inputs `( ;; propagated for development purposes - ("python" ,python-2) ;; probably superfluous - ("r" ,r) - ("redis" ,redis) - ("mysql" ,mysql) - ("gemma" ,gemma-git) - ("pylmm-gn2" ,pylmm-gn2) - ("plink2" ,plink-ng) - ("nginx" ,nginx) - ("python2-flask" ,python2-flask) - ("python2-htmlgen-gn" ,python2-htmlgen-gn) - ("python2-jinja2" ,python2-jinja2) - ("python2-sqlalchemy" ,python2-sqlalchemy) - ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) - ("python2-setuptools" ,python2-setuptools) - ("python2-scipy" ,python2-scipy) - ;; looks like python-numarray is not needed - ("python2-mysqlclient" ,python2-mysqlclient) - ("python2-numarray" ,python2-numarray) - ("python2-numpy" ,python2-numpy) - ("python2-pandas" ,python2-pandas) - ("python2-parallel" ,python2-parallel) - ("python2-passlib" ,python2-passlib) - ("python2-piddle" ,python2-piddle) - ("python2-redis" ,python2-redis) - ("python2-requests" ,python2-requests) - ("python2-rpy2" ,python2-rpy2) - ("python2-scipy" ,python2-scipy) - ("python2-simplejson" ,python2-simplejson) - ("python2-pyyaml" ,python2-pyyaml) - ("python2-xlsxwriter" ,python2-xlsxwriter) - ;; python-yolk is not needed - ("plink" ,plink) - ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) - )) - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:tests? #f)) ; no 'setup.py test' - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) - (define-public rdmd (package (name "rdmd") |