GNU bug report logs - #45873
[PATCH] gnu: Add r-snapatac.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-snapatac.
Date: Thu, 14 Jan 2021 20:57:44 +0100

* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
---
 gnu/packages/bioinformatics.scm | 51 ++++++++++++++++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 512abcd8fd..6be82773ac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2017 Arun Isaac <arunisaac <at> systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
-;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
+;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
 ;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;; Copyright © 2019 Brian Leung <bkleung89 <at> gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg <at> gnu.org>
@@ -7073,6 +7073,55 @@ sequence.")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-snapatac
+  (package
+    (name "r-snapatac")
+    (version "2.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/r3fang/SnapATAC")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+          (base32 "037jzlbl436fi7lkpq7d83i2vd1crnrik3vac2x6xj75dbikb2av"))))
+    (properties `((upstream-name . "SnapATAC")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-bigmemory" ,r-bigmemory)
+        ("r-doparallel" ,r-doparallel)
+        ("r-dosnow" ,r-dosnow)
+        ("r-edger" ,r-edger)
+        ("r-foreach" ,r-foreach)
+        ("r-genomicranges" ,r-genomicranges)
+        ("r-igraph" ,r-igraph)
+        ("r-iranges" ,r-iranges)
+        ("r-irlba" ,r-irlba)
+        ("r-matrix" ,r-matrix)
+        ("r-plyr" ,r-plyr)
+        ("r-plot3d" ,r-plot3d)
+        ("r-rann" ,r-rann)
+        ("r-raster" ,r-raster)
+        ("r-rcolorbrewer" ,r-rcolorbrewer)
+        ("r-rhdf5" ,r-rhdf5)
+        ("r-rtsne" ,r-rtsne)
+        ("r-scales" ,r-scales)
+        ("r-viridis" ,r-viridis)))
+    (home-page "https://github.com/r3fang/SnapATAC")
+    (synopsis "Single nucleus analysis package for ATAC-Seq")
+    (description
+      "This package provides a fast and accurate analysis toolkit for single
+cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing).
+Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and
+reveal cell-type specific regulatory landscapes.  However, the exceeding data
+sparsity has posed unique challenges for the data analysis.  This package
+@code{r-snapatac} is an end-to-end bioinformatics pipeline for analyzing large-
+scale single cell ATAC-seq data which includes quality control, normalization,
+clustering analysis, differential analysis, motif inference and exploration of
+single cell ATAC-seq sequencing data.")
+    (license license:gpl3)))
+
 (define-public r-scde
   (package
     (name "r-scde")
-- 
2.30.0

Message #8 received at 45873 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 45873 <at> debbugs.gnu.org
Cc: "Patrascu, Madalin Ionel" <MadalinIonel.Patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-snapatac.
Date: Fri, 15 Jan 2021 00:43:45 +0100

Hi Madalin,

thanks for the patch.  It looks good to me but I have a few questions.

The README file claims that the Python Snaptools must be installed.
This package does not do this, so I suppose the package will fail when
it’s run in an environment that does not have the Snaptools on the PATH.

Do you happen to have a package definition for the Snaptools as well, so
that we could either propagate it or patch r-snapatac to retain
references to the executables it provides?

I also see references to Homer and other bioinfo tools, which are not
provided by this package and which are not found among the inputs.  Does
it make sense to install this package when these tools are not
available?

-- 
Ricardo

Message #13 received at 45873 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 45873 <at> debbugs.gnu.org, "Patrascu,
 Madalin Ionel" <MadalinIonel.Patrascu <at> mdc-berlin.de>
Subject: Re: [bug#45873] [PATCH] gnu: Add r-snapatac.
Date: Fri, 21 Feb 2025 23:13:25 +0100

Hi Ricardo, Madalin,

Thanks for the submission.

For reference of this old submission:

    https://issues.guix.gnu.org/issue/45873

On Fri, 15 Jan 2021 at 00:43, Ricardo Wurmus <rekado <at> elephly.net> wrote:

> Do you happen to have a package definition for the Snaptools as well, so
> that we could either propagate it or patch r-snapatac to retain
> references to the executables it provides?
>
> I also see references to Homer and other bioinfo tools, which are not
> provided by this package and which are not found among the inputs.  Does
> it make sense to install this package when these tools are not
> available?

Well, what is the status?  Is it still relevant?  Or closing?

Cheers,
simon

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