GNU bug report logs -
#32984
[PATCH] gnu: Add filtlong.
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bug#32984
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guix-patches
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(Mon, 08 Oct 2018 09:19:01 GMT)
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pimi <madalinionel.patrascu <at> mdc-berlin.de>
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(Mon, 08 Oct 2018 09:19:01 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
* 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
Reply sent
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ludo <at> gnu.org (Ludovic Courtès)
:
You have taken responsibility.
(Mon, 08 Oct 2018 16:33:02 GMT)
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Notification sent
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pimi <madalinionel.patrascu <at> mdc-berlin.de>
:
bug acknowledged by developer.
(Mon, 08 Oct 2018 16:33:02 GMT)
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Message #10 received at 32984-done <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
Hello,
pimi <madalinionel.patrascu <at> 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’.
[Message part 2 (text/x-patch, inline)]
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.")
Information forwarded
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guix-patches <at> gnu.org
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bug#32984
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(Tue, 09 Oct 2018 16:24:01 GMT)
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Message #13 received at 32984 <at> debbugs.gnu.org (full text, mbox):
* 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
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guix-patches <at> gnu.org
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bug#32984
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(Thu, 11 Oct 2018 20:56:01 GMT)
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Message #16 received at 32984 <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
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! :)
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bug#32984
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(Mon, 05 Nov 2018 16:27:02 GMT)
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Message #19 received at 32984 <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
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
[Message part 2 (text/html, inline)]
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(Tue, 04 Dec 2018 12:24:05 GMT)
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This bug report was last modified 6 years and 257 days ago.
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