GNU bug report logs - #52091
[PATCH] gnu: Add ccwl.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 52091 in the body.
You can then email your comments to 52091 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: guix-patches <at> gnu.org
Cc: Arun Isaac <arunisaac <at> systemreboot.net>
Subject: [PATCH] gnu: Add ccwl.
Date: Thu, 25 Nov 2021 11:16:27 +0530

* gnu/packages/bioinformatics.scm (ccwl): New variable.
---
 gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67335daead..ec34ff0916 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -142,6 +142,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages shells)
+  #:use-module (gnu packages skribilo)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages statistics)
@@ -15886,3 +15887,37 @@ (define-public r-cytonorm
 control samples and applying quantile normalization on all markers of
 interest.")
       (license license:gpl2+))))
+
+(define-public ccwl
+  (package
+    (name "ccwl")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://ccwl.systemreboot.net/releases/ccwl-"
+                           version ".tar.lz"))
+       (sha256
+        (base32
+         "1ar8rfz3zrksgygrv67zv77y8gfvvz54zcs546jn6j28y20basla"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:make-flags '("GUILE_AUTO_COMPILE=0"))) ; to prevent guild warnings
+    (inputs
+     `(("guile" ,guile-3.0)
+       ("guile-libyaml" ,guile-libyaml)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("lzip" ,lzip)
+       ;; To build documentation
+       ("cwltool" ,cwltool)
+       ("graphviz" ,graphviz)
+       ("skribilo" ,skribilo)))
+    (home-page "https://ccwl.systemreboot.net")
+    (synopsis "Concise common workflow language")
+    (description "The @acronym{ccwl, Concise Common Workflow Language} is a
+concise syntax to express CWL workflows.  ccwl is a compiler to generate CWL
+workflows from concise descriptions in ccwl.  It is implemented as an
+@acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming
+language.")
+    (license license:gpl3+)))
-- 
2.34.0

Message #8 received at 52091 <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: 52091 <at> debbugs.gnu.org
Cc: Arun Isaac <arunisaac <at> systemreboot.net>
Subject: [PATCH v2 0/1] Add ccwl
Date: Mon, 29 Nov 2021 21:18:26 +0530

Hi,

In the last patch, I forgot to wrap the ccwl executable. I have fixed this in
the v2 patch.

Regards,
Arun

Arun Isaac (1):
  gnu: Add ccwl.

 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

-- 
2.34.0

Message #11 received at 52091 <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: 52091 <at> debbugs.gnu.org
Cc: Arun Isaac <arunisaac <at> systemreboot.net>
Subject: [PATCH v2 1/1] gnu: Add ccwl.
Date: Mon, 29 Nov 2021 21:18:27 +0530

* gnu/packages/bioinformatics.scm (ccwl): New variable.
---
 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67335daead..364fbad2cf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -142,6 +142,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages shells)
+  #:use-module (gnu packages skribilo)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages statistics)
@@ -15886,3 +15887,55 @@ (define-public r-cytonorm
 control samples and applying quantile normalization on all markers of
 interest.")
       (license license:gpl2+))))
+
+(define-public ccwl
+  (package
+    (name "ccwl")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://ccwl.systemreboot.net/releases/ccwl-"
+                           version ".tar.lz"))
+       (sha256
+        (base32
+         "1ar8rfz3zrksgygrv67zv77y8gfvvz54zcs546jn6j28y20basla"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags '("GUILE_AUTO_COMPILE=0") ; to prevent guild warnings
+       #:modules (((guix build guile-build-system)
+                   #:select (target-guile-effective-version))
+                  ,@%gnu-build-system-modules)
+       #:imported-modules ((guix build guile-build-system)
+                           ,@%gnu-build-system-modules)
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (effective-version (target-guile-effective-version)))
+               (wrap-program (string-append out "/bin/ccwl")
+                 `("GUILE_LOAD_PATH" prefix
+                   (,(string-append out "/share/guile/site/" effective-version)
+                    ,(getenv "GUILE_LOAD_PATH")))
+                 `("GUILE_LOAD_COMPILED_PATH" prefix
+                   (,(string-append out "/lib/guile/" effective-version "/site-ccache")
+                    ,(getenv "GUILE_LOAD_COMPILED_PATH"))))))))))
+    (inputs
+     `(("guile" ,guile-3.0)
+       ("guile-libyaml" ,guile-libyaml)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("lzip" ,lzip)
+       ;; To build documentation
+       ("cwltool" ,cwltool)
+       ("graphviz" ,graphviz)
+       ("skribilo" ,skribilo)))
+    (home-page "https://ccwl.systemreboot.net")
+    (synopsis "Concise common workflow language")
+    (description "The @acronym{ccwl, Concise Common Workflow Language} is a
+concise syntax to express CWL workflows.  ccwl is a compiler to generate CWL
+workflows from concise descriptions in ccwl.  It is implemented as an
+@acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming
+language.")
+    (license license:gpl3+)))
-- 
2.34.0

Message #14 received at 52091 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Arun Isaac <arunisaac <at> systemreboot.net>
Cc: 52091 <at> debbugs.gnu.org
Subject: Re: bug#52091: [PATCH] gnu: Add ccwl.
Date: Thu, 09 Dec 2021 16:30:22 +0100

Hello,

Arun Isaac <arunisaac <at> systemreboot.net> skribis:

> * gnu/packages/bioinformatics.scm (ccwl): New variable.

LGTM, go for it!

Thanks,
Ludo’.

Message #19 received at 52091-done <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: 52091-done <at> debbugs.gnu.org
Subject: Re: bug#52091: [PATCH] gnu: Add ccwl.
Date: Fri, 10 Dec 2021 15:37:04 +0530

[Message part 1 (text/plain, inline)]

Pushed after adding bash-minimal to inputs (now required due to the
wrap-program phase), thank you!

[signature.asc (application/pgp-signature, inline)]

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.