diff options
| -rw-r--r-- | .guix-channel | 6 | ||||
| -rw-r--r-- | README.org | 7 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 1 | ||||
| -rw-r--r-- | gn/packages/python24.scm | 97 | ||||
| -rw-r--r-- | gn/packages/web.scm | 2 | ||||
| -rw-r--r-- | gn/services/genenetwork.scm | 1 |
6 files changed, 15 insertions, 99 deletions
diff --git a/.guix-channel b/.guix-channel new file mode 100644 index 0000000..f19d607 --- /dev/null +++ b/.guix-channel @@ -0,0 +1,6 @@ +(channel + (version 0) + (dependencies + (channel + (name guix-past) + (url "https://gitlab.inria.fr/guix-hpc/guix-past")))) @@ -19,7 +19,7 @@ To easily use the packages from this repo, simply add it to your (cons* (channel (name 'gn-bioinformatics) - (url "https://git.genenetwork.org/pjotrp/guix-bioinformatics.git") + (url "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git") (branch "master")) %default-channels) #+END_SRC @@ -33,8 +33,9 @@ the GUIX_PACKAGE_PATH to point to the root of this directory before running Guix. E.g. #+BEGIN_SRC bash - git clone https://git.genenetwork.org/pjotrp/guix-bioinformatics.git - export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ + git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git + git clone https://gitlab.inria.fr/guix-hpc/guix-past.git + export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/:$PWD/guix-past/modules guix package -A cwl #+END_SRC diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 318cb47..e3e478b 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -31,6 +31,7 @@ #:use-module (gnu packages web) #:use-module (gnu packages wget) #:use-module (gnu packages xml) + #:use-module (past packages python) #:use-module (gn packages bioinformatics) #:use-module (gn packages twint) #:use-module (gn packages crates-io) diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm index b24190d..60807b5 100644 --- a/gn/packages/python24.scm +++ b/gn/packages/python24.scm @@ -3,111 +3,18 @@ #:use-module (guix utils) #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix git-download) #:use-module (guix build-system python) #:use-module (gn packages python) + #:use-module (past packages python) #:use-module (gnu packages compression) - #:use-module (gnu packages fontutils) - #:use-module (gnu packages ghostscript) - #:use-module (gnu packages image) #:use-module (gnu packages maths) - #:use-module (gnu packages onc-rpc) - #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) - #:use-module (gnu packages readline) - #:use-module (gnu packages tcl) - #:use-module (gnu packages tls) #:use-module (srfi srfi-1)) -;; TODO: Check against 'guix lint -c cve python2.4' list: -;; CVE-2019-9740, CVE-2019-9947, CVE-2019-9948, CVE-2018-1060, CVE-2018-1061, -;; CVE-2014-9365, CVE-2012-0845, CVE-2012-1150, CVE-2011-1521, CVE-2011-4940, -;; CVE-2010-3492, CVE-2008-5031, CVE-2008-5983 -(define-public python-2.4 - (package - (inherit python-2) - (name "python2.4") - (version "2.4.6") - (source - (origin - (method url-fetch) - (uri (string-append "https://www.python.org/ftp/python/" - version "/Python-" version ".tar.bz2")) - (sha256 - (base32 - "021y88a4ki07dgq19yhg6zfvmncfiz7h5b2255438i9zmlwl246s")))) - (outputs '("out")) - (arguments - (substitute-keyword-arguments (package-arguments python-2) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'create-setup-local - (lambda* (#:key inputs #:allow-other-keys) - (let ((zlib (assoc-ref inputs "zlib")) - (tcl (assoc-ref inputs "tcl")) - (tk (assoc-ref inputs "tk")) - (gdbm (assoc-ref inputs "gdbm")) - (read (assoc-ref inputs "readline")) - (rpc (assoc-ref inputs "libtirpc")) - (nsl (assoc-ref inputs "libnsl")) - (ssl (assoc-ref inputs "openssl"))) - (with-output-to-file "Modules/Setup.local" - (lambda _ - (format #t "readline readline.c -I~a/include -L~a/lib -lreadline~@ - _ssl _ssl.c -DUSE_SSL -I$~a/include/openssl -L~a/lib -lssl -lcrypto~@ - _tkinter _tkinter.c tkappinit.c -DWITH_APPINIT -L~a/lib -I~a/include -L~a/lib -I~a/include -ltk~a -ltcl~a~@ - gdbm gdbmmodule.c -I~a/include -L~a/lib -lgdbm~@ - nis nismodule.c -I~a/include/tirpc -I~a/include -ltirpc -lnsl~@ - zlib zlibmodule.c -I~a/include -L~a/lib -lz~%" -read read ssl ssl tcl tcl tk tk ,(version-major+minor (package-version tcl)) ,(version-major+minor (package-version tcl)) gdbm gdbm rpc nsl zlib zlib)))) - #t)) - (add-after 'unpack 'patch-rpc-location - (lambda _ - (substitute* "Modules/nismodule.c" - (("<rpc/") "<tirpc/rpc/")) - (substitute* "setup.py" - (("\\['nsl'") "['nsl', 'tirpc'")) - #t)) - (add-after 'unpack 'skip-crypt-module - (lambda _ - (substitute* "setup.py" - ((".*cryptmodule.c.*") "\n")) - #t)) - (add-before 'check 'delete-failing-tests - (lambda _ - (for-each - (lambda (file) - (delete-file (string-append "Lib/test/" file))) - '("test_anydbm.py" "test_array.py" "test_decimal.py" - "test_getargs2.py" "test_long.py" "test_math.py" - "test_mhlib.py" "test_random.py" "test_socket.py" - "test_str.py" "test_userstring.py" "test_whichdb.py" - "test_zlib.py")) - #t)) - (add-after 'check 'find-netinet-in-h - (lambda* (#:key inputs #:allow-other-keys) - (let ((glibc (assoc-ref inputs "libc"))) - (substitute* (find-files "Lib/plat-generic" ".*") - (("/usr/include/netinet/in.h") - (string-append glibc "/include/netinet/in.h"))) - #t))) - (delete 'move-tk-inter))) - ;; Python-2.4 does not support '-j'. - ((#:make-flags _) ''()))) - (native-search-paths - (list (search-path-specification - (variable "PYTHONPATH") - (files '("lib/python2.4/site-packages"))))) - (inputs - `(("libnsl" ,libnsl) - ("libtirpc" ,libtirpc) - ("openssl" ,openssl-1.0) - ,@(alist-delete "openssl" (package-inputs python-2)))))) - (define (default-python2.4) "Return the default Python-2.4 package." ;; Lazily resolve the binding. - (let ((python (resolve-interface '(gn packages python24)))) + (let ((python (resolve-interface '(past packages python)))) (module-ref python 'python-2.4))) ;; We borrow this from (guix build-system python) since we cannot refer to it diff --git a/gn/packages/web.scm b/gn/packages/web.scm index ebcd0db..9589586 100644 --- a/gn/packages/web.scm +++ b/gn/packages/web.scm @@ -4,7 +4,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages compression) #:use-module (gnu packages fonts) - #:use-module (gn packages python24) + #:use-module (past packages python) #:use-module (gnu packages python) #:use-module (gnu packages readline) #:use-module (gnu packages tcl) diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm index ac7ead4..0137e94 100644 --- a/gn/services/genenetwork.scm +++ b/gn/services/genenetwork.scm @@ -2,6 +2,7 @@ (use-modules (gnu) (ice-9 match) + (past packages python) (gn packages genenetwork) (gn packages python24) (gn packages web)) |