[bug#32984] [PATCH] gnu: Add filtlong.

[bug#32984] [PATCH] gnu: Add filtlong.

[pimi]

* gnu/packages/bioinformatics.scm (filtlong): New variable.
---
 gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab9dc185a..43cdf811e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14057,3 +14057,66 @@ absolute GSEA.")
     (description "Ngless is a domain-specific language for
 @dfn{next-generation sequencing} (NGS) data processing.")
     (license license:expat)))
+
+(define-public filtlong
+  ;; The recommended way to install is to clone the git repository
+  ;; https://github.com/rrwick/Filtlong#installation
+  ;; and the lastest release is more than nine months old
+  (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab")
+        (revision "1"))
+    (package
+      (name "filtlong")
+      (version (git-version "0.2.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rrwick/Filtlong.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
+      ;;(properties `((upstream-name . "Filtlong")))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ; no check target
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (scripts (string-append out "/scripts")))
+                 (mkdir-p bin)
+                 (mkdir-p scripts)
+                 (install-file "bin/filtlong" bin)
+                 (install-file "scripts/histogram.py" scripts)
+                 (install-file "scripts/read_info_histograms.sh" scripts))
+               #t))
+           (add-after 'install 'wrap-program
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (path (getenv "PYTHONPATH")))
+                 ;;(wrap-program (string-apend scripts "scripts/read_info_histograms.sh")
+                 (wrap-program (string-append out "/scripts/histogram.py")
+                   `("PYTHONPATH" ":" prefix (,path))))
+               #t))
+           (add-before 'check 'patch-tests
+             (lambda _
+               (substitute* "scripts/read_info_histograms.sh"
+                 (("awk") (which "gawk")))
+               #t)))))
+      (inputs
+       `(("gawk" ,gawk)                 ;for read_info_histograms.sh
+         ("python" ,python-2)           ; required for histogram.py
+         ("zlib" ,zlib)))
+      (home-page "https://github.com/rrwick/Filtlong/")
+      (synopsis "Tool for quality filtering of Nanopore and PacBio data")
+      (description
+       "The @code{filtlong} package is a tool for filtering long reads by quality.
+It can take a set of long reads and produce a smaller, better subset.  It uses
+both read length (longer is better) and read identity (higher is better) when
+choosing which reads pass the filter.")
+      (license (list license:gpl3       ;filtlong
+                     license:asl2.0))))) ;histogram.py
-- 
2.17.1

bug#32984: [PATCH] gnu: Add filtlong.

[Ludovic Courtès]

[-- Attachment #1: Type: text/plain, Size: 222 bytes --]

Hello,

pimi <madalinionel.patrascu@mdc-berlin.de> skribis:

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

Applied with the changes below; let me know if anything is amiss.

Thanks!

Ludo’.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: Type: text/x-patch, Size: 2357 bytes --]

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 43cdf811e..ed713cd14 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14076,7 +14076,6 @@ absolute GSEA.")
          (file-name (git-file-name name version))
          (sha256
           (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
-      ;;(properties `((upstream-name . "Filtlong")))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f                    ; no check target
@@ -14087,9 +14086,7 @@ absolute GSEA.")
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin"))
-                      (scripts (string-append out "/scripts")))
-                 (mkdir-p bin)
-                 (mkdir-p scripts)
+                      (scripts (string-append out "/share/filtlong/scripts")))
                  (install-file "bin/filtlong" bin)
                  (install-file "scripts/histogram.py" scripts)
                  (install-file "scripts/read_info_histograms.sh" scripts))
@@ -14098,8 +14095,8 @@ absolute GSEA.")
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (path (getenv "PYTHONPATH")))
-                 ;;(wrap-program (string-apend scripts "scripts/read_info_histograms.sh")
-                 (wrap-program (string-append out "/scripts/histogram.py")
+                 (wrap-program (string-append out
+                                              "/share/filtlong/scripts/histogram.py")
                    `("PYTHONPATH" ":" prefix (,path))))
                #t))
            (add-before 'check 'patch-tests
@@ -14114,7 +14111,7 @@ absolute GSEA.")
       (home-page "https://github.com/rrwick/Filtlong/")
       (synopsis "Tool for quality filtering of Nanopore and PacBio data")
       (description
-       "The @code{filtlong} package is a tool for filtering long reads by quality.
+       "The Filtlong package is a tool for filtering long reads by quality.
 It can take a set of long reads and produce a smaller, better subset.  It uses
 both read length (longer is better) and read identity (higher is better) when
 choosing which reads pass the filter.")

[bug#32984] [PATCH] gnu: filtlong: update path in aux script.

[pimi]

* gnu/packages/bioinformatics.scm (filtlong)[extra scritps]: corrected
the loading path for the filtlong in the script read_info_histograms.sh.
---
 gnu/packages/bioinformatics.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ed713cd14..cb9ce4df0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14103,6 +14103,8 @@ absolute GSEA.")
              (lambda _
                (substitute* "scripts/read_info_histograms.sh"
                  (("awk") (which "gawk")))
+               (substitute* "scripts/read_info_histograms.sh"
+                (("/../") "/../../../"))
                #t)))))
       (inputs
        `(("gawk" ,gawk)                 ;for read_info_histograms.sh
-- 
2.17.1

[bug#32984] [PATCH] gnu: filtlong: update path in aux script.

[Leo Famulari]

[-- Attachment #1: Type: text/plain, Size: 572 bytes --]

On Tue, Oct 09, 2018 at 06:22:39PM +0200, pimi wrote:
> * gnu/packages/bioinformatics.scm (filtlong)[extra scritps]: corrected
> the loading path for the filtlong in the script read_info_histograms.sh.

[...]

>               (lambda _
>                 (substitute* "scripts/read_info_histograms.sh"
>                   (("awk") (which "gawk")))
> +               (substitute* "scripts/read_info_histograms.sh"
> +                (("/../") "/../../../"))
>                 #t)))))

Can you add a code comment explaining the effect of this change? It's
rather cryptic! :)

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]

[bug#32984] [PATCH] gnu: filtlong: update path in aux script.

[mpatras]

[-- Attachment #1: Type: text/plain, Size: 1761 bytes --]

Hello Leo,

I am sorry for this delayed response!

In the initial version of this description, I have put the auxiliary 
scripts in /scripts/.

I didn't know that all auxiliary scripts should be put in 
/share/name_of_package/scripts.

The script loads the package using a relative path.

Ludo corrected my description and changed my substitute lines to this,

-                 (wrap-program (string-append out "/scripts/histogram.py")
+                 (wrap-program (string-append out
+                                              "/share/filtlong/scripts/histogram.py")

Now the script is on the right place 
(/share/filtlong/scripts/histogram.py), but it does not contain the 
right relative path. So, this patch is needed to correct the relative path.

+               (substitute* "scripts/read_info_histograms.sh"
+                (("/../") "/../../../"))

Sorry, from the beginning was my mistake!
On 11.10.2018 22:55, Leo Famulari wrote:
> On Tue, Oct 09, 2018 at 06:22:39PM +0200, pimi wrote:
>> * gnu/packages/bioinformatics.scm (filtlong)[extra scritps]: corrected
>> the loading path for the filtlong in the script read_info_histograms.sh.
> [...]
>
>>                (lambda _
>>                  (substitute* "scripts/read_info_histograms.sh"
>>                    (("awk") (which "gawk")))
>> +               (substitute* "scripts/read_info_histograms.sh"
>> +                (("/../") "/../../../"))
>>                  #t)))))
> Can you add a code comment explaining the effect of this change? It's
> rather cryptic! :)

-- 
All the best!

Mădălin Ionel Patrașcu

System Administrator
The Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrück Center (MDC)
Robert-Rössle-Straße 10
House 87, room 1.10
13125 Berlin, Germany


[-- Attachment #2: Type: text/html, Size: 3558 bytes --]