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# GNU Guix --- Functional package management for GNU
# Copyright © 2018, 2019 Ludovic Courtès <ludo@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/>.

#
# Test the 'guix pack --localstatedir' command-line utility.
#

guix pack --version

# 'guix pack --localstatedir' produces derivations that depend on
# guile-sqlite3 and guile-gcrypt.  To make that relatively inexpensive, run
# the test in the user's global store if possible, on the grounds that
# binaries may already be there or can be built or downloaded inexpensively.

storedir="`guile -c '(use-modules (guix config))(display %storedir)'`"
localstatedir="`guile -c '(use-modules (guix config))(display %localstatedir)'`"
NIX_STORE_DIR="$storedir"
GUIX_DAEMON_SOCKET="$localstatedir/guix/daemon-socket/socket"
export NIX_STORE_DIR GUIX_DAEMON_SOCKET

if ! guile -c '(use-modules (guix)) (exit (false-if-exception (open-connection)))'
then
    exit 77
fi

# Build a tarball with '--localstatedir'
the_pack="`guix pack -C none --localstatedir --profile-name=current-guix \
            guile-bootstrap`"
test_directory="`mktemp -d`"
trap 'chmod -Rf +w "$test_directory"; rm -rf "$test_directory"' EXIT

cd "$test_directory"
tar -xf "$the_pack"

profile="`find -name current-guix`"
test "`readlink $profile`" = "current-guix-1-link"
test -s "`dirname $profile`/../../../db/db.sqlite"
test -x ".`guix build guile-bootstrap`/bin/guile"
cd -

# Make sure the store database is not completely bogus.
guile -c "(use-modules (sqlite3) (guix config) (ice-9 match))

  (define db
    (sqlite-open (string-append \"$test_directory\"
                                %localstatedir
                               \"/guix/db/db.sqlite\")
                 SQLITE_OPEN_READONLY))

  (define stmt
    (sqlite-prepare db \"SELECT * FROM ValidPaths;\"))

  (match (sqlite-fold cons '() stmt)
    ((#(ids paths hashes times derivers sizes) ...)
     (exit (member \"`guix build guile-bootstrap`\" paths))))"
Add r-rnaseqdtu.
* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm37
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e9778831d2..106b25a50b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9009,6 +9009,43 @@ for analyzing gene-level association tests in meta-analyses for binary
trait.")
(license license:gpl3)))
+(define-public r-rnaseqdtu
+ (let ((commit "5bee1e769d2e1dc6a3f1cecb78078050eeb5b9ac")
+ (revision "1"))
+ (package
+ (name "r-rnaseqdtu")
+ (version (git-version "2.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mikelove/rnaseqDTU/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0jfi1ydsk8m5nadwnih48v87nnxdc7s3f0pny4axmnj40dd42as0"))))
+ (properties `((upstream-name . "rnaseqDTU")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-deseq2
+ r-devtools
+ r-dexseq
+ r-drimseq
+ r-edger
+ r-rafalib
+ r-stager))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/mikelove/rnaseqDTU/")
+ (synopsis "RNA-seq workflow for differential transcript usage")
+ (description
+ "This package provides an RNA-seq workflow for differential transcript
+usage (DTU) following Salmon quantification. This workflow performs a DTU
+analysis on simulated data. It also shows how to use stageR to perform
+two-stage testing of DTU, a statistical framework to screen at the gene level
+and then confirm which transcripts within the significant genes show evidence
+of DTU.")
+ (license license:artistic2.0))))
+
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))