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authorpjotrp2017-02-26 18:48:20 +0000
committerpjotrp2017-02-26 18:48:27 +0000
commit699b05703c743baf51f720db22eb0a2438cb8cad (patch)
tree62d7d27486a2fb698e81cd4b6bfba461d3b7d634 /gn/packages
parent728073454851da222401d6ad283762c8307fcf96 (diff)
downloadguix-bioinformatics-699b05703c743baf51f720db22eb0a2438cb8cad.tar.gz
Updating packages
- Removed slurm as it is in mainline now
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/slurm.scm100
-rw-r--r--gn/packages/statistics.scm2
-rw-r--r--gn/packages/tcl.scm2
3 files changed, 2 insertions, 102 deletions
diff --git a/gn/packages/slurm.scm b/gn/packages/slurm.scm
deleted file mode 100644
index 9e3d063..0000000
--- a/gn/packages/slurm.scm
+++ /dev/null
@@ -1,100 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015 Roel Janssen <roel@gnu.org>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gn packages slurm)
- #:use-module ((guix licenses) #:prefix license:)
- #:use-module (gnu packages)
- #:use-module (guix packages)
- #:use-module (guix download)
- #:use-module (guix build-system gnu)
- #:use-module (gnu packages tcl)
- #:use-module (gnu packages linux)
- #:use-module (gnu packages textutils)
- #:use-module (gnu packages base)
- #:use-module (gnu packages gnupg)
- #:use-module (gnu packages libedit)
- #:use-module (gnu packages llvm)
- #:use-module (gnu packages perl)
- #:use-module (gnu packages python)
- #:use-module (gnu packages tls)
- #:use-module (gnu packages zip)
- #:use-module (guix git-download))
-
-(define-public slurm-llnl
- (package
- (name "slurm-llnl")
- (version "15-08-6-1")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "1h8al21blmrhma9r7qxkba2g5i74m3hrjc9a640j7px54szvg18v"))))
- (inputs `(("openssl" ,openssl)
- ("munge" ,munge)
- ("perl" ,perl)
- ("expect" ,expect)
- ("python" ,python)
- ("linux-pam" , linux-pam)))
- (build-system gnu-build-system)
- (arguments
- `(#:configure-flags '("--enable-pam")
- #:phases
- (modify-phases %standard-phases
- (add-before
- 'configure 'rewrite-usr-bin
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "./doc/html/shtml2html.py"
- (("#!/usr/bin/env python")
- (string-append "#!" (which "python3"))))
- (substitute* "src/common/env.c"
- (("/usr/bin/env") (which "env"))))))))
- (home-page "http://www.schedmd.com/")
- (synopsis "Tool for cluster computing")
- (description
- "Fault-tolerant, and highly scalable cluster management and job
-scheduling system for large and small clusters.")
- (license license:gpl2+)))
-
-(define-public munge
- (package
- (name "munge")
- (version "0.5.11")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/dun/munge/archive/munge-"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0njplyalwwqh7xr7xc7klc6x06mq0ak8w2pxh85w8n4hxkmqqnf5"))))
- (inputs `(("openssl" ,openssl)
- ("libgcrypt" ,libgcrypt)))
- (build-system gnu-build-system)
- (home-page "https://dun.github.io/munge/")
- (synopsis "Scalable authentication service for creating and validating
-credentials on a cluster")
- (description "Munge allows a process to authenticate the UID and
-GID of another local or remote process within a group of hosts having
-common users and groups. These hosts form a security realm that is
-defined by a shared cryptographic key. Clients within this security
-realm can create and validate credentials without the use of root
-privileges, reserved ports, or platform-specific methods.")
- (license license:gpl2+)))
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index b83ccf2..4af5cc5 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -364,7 +364,7 @@
for use in genome-wide association studies (GWAS).")
(license license:agpl3+))))
-(define-public r-ctl
+(define-public r-ctl ; guix: ready
(package
(name "r-ctl")
(version "1.0.0-0")
diff --git a/gn/packages/tcl.scm b/gn/packages/tcl.scm
index 9b1cb5a..d71c1c6 100644
--- a/gn/packages/tcl.scm
+++ b/gn/packages/tcl.scm
@@ -13,7 +13,7 @@
#:use-module (gnu packages xorg)
#:use-module (guix licenses))
-(define-public environment-modules
+(define-public environment-modules ; guix: fix DL and tests
(package
(name "environment-modules")
(version "3.2.10")