[PATCH]: gnu: Add HISAT.

[PATCH]: gnu: Add HISAT.

[Ricardo Wurmus]

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Attached is a patch to add HISAT, another popular read aligner.

I would have really liked to use snippets here for a few static changes
to the sources, but it seems that snippets cannot be used with zip
archives (see my earlier message to the mailing list).

~~ Ricardo


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From 305768bfef9bf4bc8d57828e27b8439dedd574bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 9 Feb 2015 12:13:26 +0100
Subject: [PATCH] gnu: Add HISAT.

* gnu/packages/bioinformatics.scm (hisat): New variable.
---
 gnu/packages/bioinformatics.scm | 77 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 76 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c0d1438..425558d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -29,8 +29,9 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages python))
+  #:use-module (gnu packages python)
   #:use-module (gnu packages tbb)
+  #:use-module (gnu packages zip))
 
 (define-public bedtools
   (package
@@ -181,6 +182,80 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
 Illumina, Roche 454, and the SOLiD platform.")
     (license license:gpl3)))
 
+(define-public hisat
+  (package
+    (name "hisat")
+    (version "0.1.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
+                    version "-beta-source.zip"))
+              (sha256
+               (base32
+                "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ;no check target
+       #:make-flags '("allall")
+       #:phases
+       (alist-replace
+        'unpack
+        (lambda* (#:key source #:allow-other-keys)
+          (and (zero? (system* "unzip" source))
+               (chdir "hisat-0.1.4-beta")))
+        (alist-cons-after
+         'unpack 'patch-sources
+         (lambda _
+           ;; XXX Cannot use snippet because zip files are not supported
+           (substitute* "Makefile"
+             (("^CC = .*$") "CC = gcc")
+             (("^CPP = .*$") "CPP = g++")
+             ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+             (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+             (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
+           (substitute* '("hisat-build" "hisat-inspect")
+             (("/usr/bin/env") (which "env"))))
+         (alist-replace
+          'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+              (mkdir-p bin)
+              (for-each (lambda (file)
+                          (copy-file file (string-append bin file)))
+                        '("hisat"
+                          "hisat-build"
+                          "hisat-build-s"
+                          "hisat-build-l"
+                          "hisat-align-s"
+                          "hisat-align-l"
+                          "hisat-inspect"
+                          "hisat-inspect-s"
+                          "hisat-inspect-l"
+                          "hisat-build-s-debug"
+                          "hisat-build-l-debug"
+                          "hisat-align-s-debug"
+                          "hisat-align-l-debug"
+                          "hisat-inspect-s-debug"
+                          "hisat-inspect-l-debug"))))
+          (alist-delete 'configure %standard-phases))))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (inputs
+     `(("perl" ,perl)
+       ("python" ,python)
+       ("zlib" ,zlib)))
+    (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
+    (synopsis "Hierarchical indexing for spliced alignment of transcripts")
+    (description
+     "HISAT is a fast and sensitive spliced alignment program for mapping
+RNA-seq reads.  In addition to one global FM index that represents a whole
+genome, HISAT uses a large set of small FM indexes that collectively cover the
+whole genome.  These small indexes (called local indexes) combined with
+several alignment strategies enable effective alignment of RNA-seq reads, in
+particular, reads spanning multiple exons.")
+    (license license:gpl3)))
+
 (define-public samtools
   (package
     (name "samtools")
-- 
2.1.0

Re: [PATCH]: gnu: Add HISAT.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 305768bfef9bf4bc8d57828e27b8439dedd574bd Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 9 Feb 2015 12:13:26 +0100
> Subject: [PATCH] gnu: Add HISAT.
>
> * gnu/packages/bioinformatics.scm (hisat): New variable.

Overall looks good to me.  A couple of comments:

> +         (alist-replace
> +          'install
> +          (lambda* (#:key outputs #:allow-other-keys)
> +            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
> +              (mkdir-p bin)
> +              (for-each (lambda (file)
> +                          (copy-file file (string-append bin file)))
> +                        '("hisat"
> +                          "hisat-build"
> +                          "hisat-build-s"
> +                          "hisat-build-l"
> +                          "hisat-align-s"
> +                          "hisat-align-l"
> +                          "hisat-inspect"
> +                          "hisat-inspect-s"
> +                          "hisat-inspect-l"
> +                          "hisat-build-s-debug"
> +                          "hisat-build-l-debug"
> +                          "hisat-align-s-debug"
> +                          "hisat-align-l-debug"
> +                          "hisat-inspect-s-debug"
> +                          "hisat-inspect-l-debug"))))

If it’s possible to avoid the whole list using ‘find-files’ or
‘scandir’, that would be nicer IMO.  If it’s not, that’s fine.

> +    (license license:gpl3)))

GPLv3-only?

Thanks!

Ludo’.

Re: [PATCH]: gnu: Add HISAT.

[Ricardo Wurmus]

Ludovic Courtès writes:

> If it’s possible to avoid the whole list using ‘find-files’ or
> ‘scandir’, that would be nicer IMO.  If it’s not, that’s fine.


>
>> +    (license license:gpl3)))
>
> GPLv3-only?
>
> Thanks!
>
> Ludo’.

Re: [PATCH]: gnu: Add HISAT.

[Ricardo Wurmus]

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Ludovic Courtès writes:

> If it’s possible to avoid the whole list using ‘find-files’ or
> ‘scandir’, that would be nicer IMO.  If it’s not, that’s fine.

In the attached patch I used `find-files' instead.  The expression is a
bit long, but I think it's still clear enough to be preferable to the
long list.

>> +    (license license:gpl3)))
>
> GPLv3-only?

You were right: it's GPLv3+.  My apologies.


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From 5696a8227d98d60d38f0ff19b40a21ccb13e53f1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 9 Feb 2015 12:13:26 +0100
Subject: [PATCH] gnu: Add HISAT.

* gnu/packages/bioinformatics.scm (hisat): New variable.
---
 gnu/packages/bioinformatics.scm | 66 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 65 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c0d1438..9219bc2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -29,8 +29,9 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages python))
+  #:use-module (gnu packages python)
   #:use-module (gnu packages tbb)
+  #:use-module (gnu packages zip))
 
 (define-public bedtools
   (package
@@ -181,6 +182,69 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
 Illumina, Roche 454, and the SOLiD platform.")
     (license license:gpl3)))
 
+(define-public hisat
+  (package
+    (name "hisat")
+    (version "0.1.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
+                    version "-beta-source.zip"))
+              (sha256
+               (base32
+                "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ;no check target
+       #:make-flags '("allall")
+       #:phases
+       (alist-replace
+        'unpack
+        (lambda* (#:key source #:allow-other-keys)
+          (and (zero? (system* "unzip" source))
+               (chdir "hisat-0.1.4-beta")))
+        (alist-cons-after
+         'unpack 'patch-sources
+         (lambda _
+           ;; XXX Cannot use snippet because zip files are not supported
+           (substitute* "Makefile"
+             (("^CC = .*$") "CC = gcc")
+             (("^CPP = .*$") "CPP = g++")
+             ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+             (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+             (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
+           (substitute* '("hisat-build" "hisat-inspect")
+             (("/usr/bin/env") (which "env"))))
+         (alist-replace
+          'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+              (mkdir-p bin)
+              (for-each
+               (lambda (file)
+                 (copy-file file (string-append bin file)))
+               (find-files
+                "."
+                "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
+          (alist-delete 'configure %standard-phases))))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (inputs
+     `(("perl" ,perl)
+       ("python" ,python)
+       ("zlib" ,zlib)))
+    (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
+    (synopsis "Hierarchical indexing for spliced alignment of transcripts")
+    (description
+     "HISAT is a fast and sensitive spliced alignment program for mapping
+RNA-seq reads.  In addition to one global FM index that represents a whole
+genome, HISAT uses a large set of small FM indexes that collectively cover the
+whole genome.  These small indexes (called local indexes) combined with
+several alignment strategies enable effective alignment of RNA-seq reads, in
+particular, reads spanning multiple exons.")
+    (license license:gpl3+)))
+
 (define-public samtools
   (package
     (name "samtools")
-- 
2.1.0

Re: [PATCH]: gnu: Add HISAT.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 5696a8227d98d60d38f0ff19b40a21ccb13e53f1 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 9 Feb 2015 12:13:26 +0100
> Subject: [PATCH] gnu: Add HISAT.
>
> * gnu/packages/bioinformatics.scm (hisat): New variable.

LGTM, thanks!

Ludo’.

Re: [PATCH]: gnu: Add HISAT.

[Andreas Enge]

Hello,

the package fails to build on i686:
   http://hydra.gnu.org/build/247325
Could you maybe have a look?

Andreas

Re: [PATCH]: gnu: Add HISAT.

[Ricardo Wurmus]

Andreas Enge writes:

> the package fails to build on i686:
>    http://hydra.gnu.org/build/247325
> Could you maybe have a look?

Thanks for notifying me.

A recurring error is apparently related to embedded assembly
instructions:

~~~~~
...
bt2_idx.h: Assembler messages:
bt2_idx.h:489: Error: invalid instruction suffix for `popcnt'
...
~~~~~

I wrote the author an email to ask whether this can be fixed upstream
for other architectures than x86_64.  Until then should I just declare
x86_64 as the only supported architecture?

~~ Ricardo

Re: [PATCH]: gnu: Add HISAT.

[Andreas Enge]

On Wed, Feb 11, 2015 at 05:14:13PM +0100, Ricardo Wurmus wrote:
> A recurring error is apparently related to embedded assembly
> instructions:
> I wrote the author an email to ask whether this can be fixed upstream
> for other architectures than x86_64.  Until then should I just declare
> x86_64 as the only supported architecture?

I would say so. On their homepage, besides the source code they provide
binaries, but only for "Linux x86_64" and "Mac OS X x86_64". I am not
surprised that high performance computing tools require a high performance
platform. Probably it is not interesting anyway to run the code on other
architectures.

Andreas

Re: [PATCH]: gnu: Add HISAT.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> I wrote the author an email to ask whether this can be fixed upstream
> for other architectures than x86_64.  Until then should I just declare
> x86_64 as the only supported architecture?

Probably yes, with a comment pointing to this discussion and possibly
the one with the author(s).

Thanks,
Ludo’.

Re: [PATCH]: gnu: Add HISAT.

[Ricardo Wurmus]

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Ludovic Courtès writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> I wrote the author an email to ask whether this can be fixed upstream
>> for other architectures than x86_64.  Until then should I just declare
>> x86_64 as the only supported architecture?
>
> Probably yes, with a comment pointing to this discussion and possibly
> the one with the author(s).

This may not even be necessary; the developer replied with a hint and
attached is a patch that should fix the build on non-x86_64
architectures.  It builds fine locally with

    ./pre-inst-env guix build --system=i686-linux hisat

Does this look okay?

~~ Ricardo


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From 5a73d260fcff839f5d07ef4ae684c78c4660f3d3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 12 Feb 2015 11:58:40 +0100
Subject: [PATCH] gnu: hisat: fix build on non-x86_64.

* gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to
  make-flags on architectures other than x86_64.
---
 gnu/packages/bioinformatics.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 48bb9dd..f384cb8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -252,8 +252,15 @@ Illumina, Roche 454, and the SOLiD platform.")
                 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f ;no check target
-       #:make-flags '("allall")
+     `(#:tests? #f ;no check target
+       #:make-flags '("allall"
+                      ;; Disable unsupported `popcnt' instructions on
+                      ;; architectures other than x86_64
+                      ,@(if (string-prefix? "x86_64"
+                                            (or (%current-target-system)
+                                                (%current-system)))
+                            '()
+                            '("POPCNT_CAPABILITY=0")))
        #:phases
        (alist-replace
         'unpack
-- 
2.1.0

Re: [PATCH]: gnu: Add HISAT.

[Andreas Enge]

On Thu, Feb 12, 2015 at 12:04:22PM +0100, Ricardo Wurmus wrote:
> This may not even be necessary; the developer replied with a hint and
> attached is a patch that should fix the build on non-x86_64
> architectures.  It builds fine locally with
>     ./pre-inst-env guix build --system=i686-linux hisat

This looks good, you could push it, and then we can see whether it will
be enough on mips.

Andreas

Re: [PATCH]: gnu: Add HISAT.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> This may not even be necessary; the developer replied with a hint and
> attached is a patch that should fix the build on non-x86_64
> architectures.  It builds fine locally with
>
>     ./pre-inst-env guix build --system=i686-linux hisat
>
> Does this look okay?

[...]

> From 5a73d260fcff839f5d07ef4ae684c78c4660f3d3 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 12 Feb 2015 11:58:40 +0100
> Subject: [PATCH] gnu: hisat: fix build on non-x86_64.
>
> * gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to
>   make-flags on architectures other than x86_64.

Definitely, yes.

Thanks for investigating,
Ludo’.