[PATCH] Add preseq.

[PATCH] Add preseq.

[Ricardo Wurmus]

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From 7e0352fad776f1c491882647ee3ad5f5319e1164 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: [PATCH] gnu: Add preseq.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 09534a8..3d36120 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2004,6 +2004,57 @@ Databases are stored in a portable image within the file system, and can be
 accessed/downloaded on demand across HTTP.")
     (license license:public-domain)))
 
+(define-public preseq
+  (package
+    (name "preseq")
+    (version "1.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "http://smithlabresearch.org/downloads/preseq-"
+                              version ".tar.bz2"))
+              (sha256
+               (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Remove bundled samtools.
+               ;; FIXME: Without samtools sources "bam2mr" is not built.
+               '(delete-file-recursively "preseq-master/samtools"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after
+          'unpack 'enter-dir
+          (lambda _
+            (chdir "preseq-master")
+            #t))
+         (replace 'configure
+                  (lambda* (#:key inputs #:allow-other-keys)
+                    ;; Fix install target
+                    (substitute* "Makefile"
+                      (("\\$\\(ROOT\\)/bin") "$(PREFIX)/bin"))
+                    #t)))
+       #:make-flags (list (string-append "PREFIX="
+                                         (assoc-ref %outputs "out"))
+                          ;; Do not attempt to link samtools objects
+                          "SAMTOOLS_DIR=")))
+    (inputs
+     `(("gsl" ,gsl)
+       ("zlib" ,zlib)))
+    (home-page "http://smithlabresearch.org/software/preseq/")
+    (synopsis "Program for analyzing library complexity")
+    (description
+     "The preseq package is aimed at predicting and estimating the complexity
+of a genomic sequencing library, equivalent to predicting and estimating the
+number of redundant reads from a given sequencing depth and how many will be
+expected from additional sequencing using an initial sequencing experiment.
+The estimates can then be used to examine the utility of further sequencing,
+optimize the sequencing depth, or to screen multiple libraries to avoid low
+complexity samples.")
+    (license license:gpl3+)))
+
 (define-public sra-tools
   (package
     (name "sra-tools")
-- 
2.1.0

Re: [PATCH] Add preseq.

[Ricardo Wurmus]

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Attached is a new version that includes support for BAM files, but
without using the bundled version of samtools.  Two patches were
necessary that I have submitted upstream.

I'm still testing this with a user, and I'm waiting for upstream to
comment on the patches, so I'm not in a hurry to push this.

~~ Ricardo


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From 3ffe6847848f6ba107e0757728f1c6a6e7807d56 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: [PATCH] gnu: Add preseq.

* gnu/packages/bioinformatics.scm (preseq): New variable.
---
 gnu/packages/bioinformatics.scm                    | 51 ++++++++++++++++++++++
 .../patches/preseq-1.0.2-install-to-PREFIX.patch   | 37 ++++++++++++++++
 .../patches/preseq-1.0.2-link-with-libbam.patch    | 33 ++++++++++++++
 3 files changed, 121 insertions(+)
 create mode 100644 gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
 create mode 100644 gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4eb977b..d6fb32c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2033,6 +2033,57 @@ Databases are stored in a portable image within the file system, and can be
 accessed/downloaded on demand across HTTP.")
     (license license:public-domain)))
 
+(define-public preseq
+  (package
+    (name "preseq")
+    (version "1.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "http://smithlabresearch.org/downloads/preseq-"
+                              version ".tar.bz2"))
+              (sha256
+               (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
+              (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
+                             (search-patch "preseq-1.0.2-link-with-libbam.patch")))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Remove bundled samtools.  Leave the headers.
+               '(for-each delete-file
+                          (find-files "preseq-master/samtools"
+                                      "\\.c$")))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after
+          'unpack 'enter-dir
+          (lambda _
+            (chdir "preseq-master")
+            #t))
+         (delete 'configure))
+       #:make-flags (list (string-append "PREFIX="
+                                         (assoc-ref %outputs "out"))
+                          (string-append "LIBBAM="
+                                         (assoc-ref %build-inputs "samtools")
+                                         "/lib/libbam.a"))))
+    (inputs
+     `(("gsl" ,gsl)
+       ("samtools" ,samtools-0.1)
+       ("zlib" ,zlib)))
+    (home-page "http://smithlabresearch.org/software/preseq/")
+    (synopsis "Program for analyzing library complexity")
+    (description
+     "The preseq package is aimed at predicting and estimating the complexity
+of a genomic sequencing library, equivalent to predicting and estimating the
+number of redundant reads from a given sequencing depth and how many will be
+expected from additional sequencing using an initial sequencing experiment.
+The estimates can then be used to examine the utility of further sequencing,
+optimize the sequencing depth, or to screen multiple libraries to avoid low
+complexity samples.")
+    (license license:gpl3+)))
+
 (define-public sra-tools
   (package
     (name "sra-tools")
diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
new file mode 100644
index 0000000..f8318ae
--- /dev/null
+++ b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
@@ -0,0 +1,37 @@
+This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
+
+From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001
+From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
+Date: Thu, 25 Jun 2015 15:01:53 +0200
+Subject: [PATCH] Install to PREFIX
+
+---
+ Makefile | 8 ++++++--
+ 1 file changed, 6 insertions(+), 2 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 4d0367a..e334f2f 100644
+--- a/preseq-master/Makefile
++++ b/preseq-master/Makefile
+@@ -22,6 +22,10 @@ ifndef ROOT
+ ROOT = $(shell pwd)
+ endif
+ 
++ifndef PREFIX
++PREFIX = $(ROOT)
++endif
++
+ ifndef SMITHLAB_CPP
+ SMITHLAB_CPP=$(ROOT)/smithlab_cpp/
+ endif
+@@ -91,8 +95,8 @@ endif
+ 	$(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS)
+ 
+ install: $(PROGS)
+-	@mkdir -p $(ROOT)/bin
+-	@install -m 755 $(PROGS) $(ROOT)/bin
++	@mkdir -p $(PREFIX)/bin
++	@install -m 755 $(PROGS) $(PREFIX)/bin
+ 
+ clean:
+ 	@-rm -f $(PROGS) *.o *~
diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
new file mode 100644
index 0000000..035a3b1
--- /dev/null
+++ b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
@@ -0,0 +1,33 @@
+This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
+
+From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001
+From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
+Date: Thu, 25 Jun 2015 15:02:35 +0200
+Subject: [PATCH] Link with libbam.a if provided via LIBBAM
+
+---
+ Makefile | 7 +++++++
+ 1 file changed, 7 insertions(+)
+
+diff --git a/Makefile b/Makefile
+index e334f2f..de310e4 100644
+--- a/preseq-master/Makefile
++++ b/preseq-master/Makefile
+@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \
+ preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
+ 
+ ifdef SAMTOOLS_DIR
++ifdef LIBBAM
++LIBS += -pthread
++bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
++        $(LIBBAM)
++else
+ bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
+         $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \
+         faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o)
+ endif
++endif # SAMTOOLS_DIR
++
+ 
+ %.o: %.cpp %.hpp
+ 	$(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)
-- 
2.1.0

Re: [PATCH] Add preseq.

[Ludovic Courtès]

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

> From 3ffe6847848f6ba107e0757728f1c6a6e7807d56 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 23 Jun 2015 10:54:00 +0200
> Subject: [PATCH] gnu: Add preseq.
>
> * gnu/packages/bioinformatics.scm (preseq): New variable.

[...]

> +              (snippet
> +               ;; Remove bundled samtools.  Leave the headers.
> +               '(for-each delete-file
> +                          (find-files "preseq-master/samtools"
> +                                      "\\.c$")))))

Why leave the headers?  Isn’t it risky to leave headers that may be
different from the Samtools that we’re actually linking against?

Otherwise LGTM.

Thanks,
Ludo’.

Re: [PATCH] Add preseq.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

>> +              (snippet
>> +               ;; Remove bundled samtools.  Leave the headers.
>> +               '(for-each delete-file
>> +                          (find-files "preseq-master/samtools"
>> +                                      "\\.c$")))))
>
> Why leave the headers?  Isn’t it risky to leave headers that may be
> different from the Samtools that we’re actually linking against?

The problem is with our Samtools package(s).  They don't install
headers.  I'd better update them to install the headers; then I could
just delete the complete "samtools" directory.

Re: [PATCH] Add preseq.

[Ludovic Courtès]

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

> Ludovic Courtès <ludo@gnu.org> writes:
>
>>> +              (snippet
>>> +               ;; Remove bundled samtools.  Leave the headers.
>>> +               '(for-each delete-file
>>> +                          (find-files "preseq-master/samtools"
>>> +                                      "\\.c$")))))
>>
>> Why leave the headers?  Isn’t it risky to leave headers that may be
>> different from the Samtools that we’re actually linking against?
>
> The problem is with our Samtools package(s).  They don't install
> headers.  I'd better update them to install the headers; then I could
> just delete the complete "samtools" directory.

Yes that would be best, if that’s fine with you.

Ludo’.

Re: [PATCH] Add preseq.

[Ricardo Wurmus]

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>>> Why leave the headers?  Isn’t it risky to leave headers that may be
>>> different from the Samtools that we’re actually linking against?
>>
>> The problem is with our Samtools package(s).  They don't install
>> headers.  I'd better update them to install the headers; then I could
>> just delete the complete "samtools" directory.
>
> Yes that would be best, if that’s fine with you.

Attached is a patch to add a build phase to samtools to install the
headers into $out/include/samtools/.

The second patch is just the updated patch for adding preseq.


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From b1ba27153faca9bdf46d42046c43f8c60f945368 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 2 Jul 2015 15:53:47 +0200
Subject: [PATCH 1/2] gnu: samtools: Install headers.

* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
  "install-headers" to install header files.
---
 gnu/packages/bioinformatics.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a1804a..ce2f55b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1824,6 +1824,10 @@ distribution, coverage uniformity, strand specificity, etc.")
        ;; systems.
        #:tests? ,(string=? (or (%current-system) (%current-target-system))
                            "x86_64-linux")
+       #:modules ((ice-9 ftw)
+                  (ice-9 regex)
+                  (guix build gnu-build-system)
+                  (guix build utils))
        #:make-flags (list "LIBCURSES=-lncurses"
                           (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
@@ -1848,7 +1852,18 @@ distribution, coverage uniformity, strand specificity, etc.")
            (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
              (mkdir-p lib)
              (copy-file "libbam.a" (string-append lib "/libbam.a"))))
-         (alist-delete 'configure %standard-phases)))))
+         (alist-cons-after
+          'install 'install-headers
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((include (string-append (assoc-ref outputs "out")
+                                          "/include/samtools/")))
+              (mkdir-p include)
+              (for-each (lambda (file)
+                          (copy-file file (string-append include
+                                                         (basename file))))
+                        (scandir "." (lambda (name) (string-match "\\.h$" name))))
+              #t))
+          (alist-delete 'configure %standard-phases))))))
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs `(("ncurses" ,ncurses)
               ("perl" ,perl)
-- 
2.1.0


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From e3bd0a861121c441b44d77d30f2aaddb766b49c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 23 Jun 2015 10:54:00 +0200
Subject: [PATCH 2/2] gnu: Add preseq.

* gnu/packages/bioinformatics.scm (preseq): New variable.
---
 gnu/packages/bioinformatics.scm                    | 56 ++++++++++++++++++++++
 .../patches/preseq-1.0.2-install-to-PREFIX.patch   | 37 ++++++++++++++
 .../patches/preseq-1.0.2-link-with-libbam.patch    | 33 +++++++++++++
 3 files changed, 126 insertions(+)
 create mode 100644 gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
 create mode 100644 gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ce2f55b..27b847e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2137,6 +2137,62 @@ subsequent visualization, annotation and storage of results.")
     ;; LGPLv2.1+
     (license (list license:gpl2 license:lgpl2.1+))))
 
+(define-public preseq
+  (package
+    (name "preseq")
+    (version "1.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "http://smithlabresearch.org/downloads/preseq-"
+                              version ".tar.bz2"))
+              (sha256
+               (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
+              (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
+                             (search-patch "preseq-1.0.2-link-with-libbam.patch")))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Remove bundled samtools.
+               '(delete-file-recursively "preseq-master/samtools"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after
+          'unpack 'enter-dir
+          (lambda _
+            (chdir "preseq-master")
+            #t))
+         (add-after
+          'unpack 'use-samtools-headers
+          (lambda _
+            (substitute* '("smithlab_cpp/SAM.cpp"
+                           "smithlab_cpp/SAM.hpp")
+              (("sam.h") "samtools/sam.h"))
+            #t))
+         (delete 'configure))
+       #:make-flags (list (string-append "PREFIX="
+                                         (assoc-ref %outputs "out"))
+                          (string-append "LIBBAM="
+                                         (assoc-ref %build-inputs "samtools")
+                                         "/lib/libbam.a"))))
+    (inputs
+     `(("gsl" ,gsl)
+       ("samtools" ,samtools-0.1)
+       ("zlib" ,zlib)))
+    (home-page "http://smithlabresearch.org/software/preseq/")
+    (synopsis "Program for analyzing library complexity")
+    (description
+     "The preseq package is aimed at predicting and estimating the complexity
+of a genomic sequencing library, equivalent to predicting and estimating the
+number of redundant reads from a given sequencing depth and how many will be
+expected from additional sequencing using an initial sequencing experiment.
+The estimates can then be used to examine the utility of further sequencing,
+optimize the sequencing depth, or to screen multiple libraries to avoid low
+complexity samples.")
+    (license license:gpl3+)))
+
 (define-public sra-tools
   (package
     (name "sra-tools")
diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
new file mode 100644
index 0000000..f8318ae
--- /dev/null
+++ b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
@@ -0,0 +1,37 @@
+This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
+
+From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001
+From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
+Date: Thu, 25 Jun 2015 15:01:53 +0200
+Subject: [PATCH] Install to PREFIX
+
+---
+ Makefile | 8 ++++++--
+ 1 file changed, 6 insertions(+), 2 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 4d0367a..e334f2f 100644
+--- a/preseq-master/Makefile
++++ b/preseq-master/Makefile
+@@ -22,6 +22,10 @@ ifndef ROOT
+ ROOT = $(shell pwd)
+ endif
+ 
++ifndef PREFIX
++PREFIX = $(ROOT)
++endif
++
+ ifndef SMITHLAB_CPP
+ SMITHLAB_CPP=$(ROOT)/smithlab_cpp/
+ endif
+@@ -91,8 +95,8 @@ endif
+ 	$(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS)
+ 
+ install: $(PROGS)
+-	@mkdir -p $(ROOT)/bin
+-	@install -m 755 $(PROGS) $(ROOT)/bin
++	@mkdir -p $(PREFIX)/bin
++	@install -m 755 $(PROGS) $(PREFIX)/bin
+ 
+ clean:
+ 	@-rm -f $(PROGS) *.o *~
diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
new file mode 100644
index 0000000..035a3b1
--- /dev/null
+++ b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
@@ -0,0 +1,33 @@
+This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
+
+From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001
+From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
+Date: Thu, 25 Jun 2015 15:02:35 +0200
+Subject: [PATCH] Link with libbam.a if provided via LIBBAM
+
+---
+ Makefile | 7 +++++++
+ 1 file changed, 7 insertions(+)
+
+diff --git a/Makefile b/Makefile
+index e334f2f..de310e4 100644
+--- a/preseq-master/Makefile
++++ b/preseq-master/Makefile
+@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \
+ preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
+ 
+ ifdef SAMTOOLS_DIR
++ifdef LIBBAM
++LIBS += -pthread
++bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
++        $(LIBBAM)
++else
+ bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
+         $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \
+         faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o)
+ endif
++endif # SAMTOOLS_DIR
++
+ 
+ %.o: %.cpp %.hpp
+ 	$(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)
-- 
2.1.0

Re: [PATCH] Add preseq.

[Ludovic Courtès]

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

> From b1ba27153faca9bdf46d42046c43f8c60f945368 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 2 Jul 2015 15:53:47 +0200
> Subject: [PATCH 1/2] gnu: samtools: Install headers.
>
> * gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
>   "install-headers" to install header files.

OK.

> From e3bd0a861121c441b44d77d30f2aaddb766b49c2 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 23 Jun 2015 10:54:00 +0200
> Subject: [PATCH 2/2] gnu: Add preseq.
>
> * gnu/packages/bioinformatics.scm (preseq): New variable.

Please add the .patch files to the commit log and to the .am file.

OK with this change.

Thank you!

Ludo’.

Re: [PATCH] Add preseq.

[Mark H Weaver]

ludo@gnu.org (Ludovic Courtès) writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From e3bd0a861121c441b44d77d30f2aaddb766b49c2 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 23 Jun 2015 10:54:00 +0200
>> Subject: [PATCH 2/2] gnu: Add preseq.
>>
>> * gnu/packages/bioinformatics.scm (preseq): New variable.
>
> Please add the .patch files to the commit log and to the .am file.
>
> OK with this change.

preseq failed to build on Hydra on x86_64 and mips64el.  As I write
this, the results are not yet in for i686.

  http://hydra.gnu.org:3000/job/gnu/master/preseq-1.0.2.x86_64-linux
  http://hydra.gnu.org:3000/job/gnu/master/preseq-1.0.2.mips64el-linux
  http://hydra.gnu.org:3000/job/gnu/master/preseq-1.0.2.i686-linux

Here's the relevant build log excerpt for x86_64:

--8<---------------cut here---------------start------------->8---
starting phase `use-samtools-headers'
Backtrace:
In ice-9/boot-9.scm:
 157: 15 [catch #t #<catch-closure 27d5580> ...]
In unknown file:
   ?: 14 [apply-smob/1 #<catch-closure 27d5580>]
In ice-9/boot-9.scm:
  63: 13 [call-with-prompt prompt0 ...]
In ice-9/eval.scm:
 432: 12 [eval # #]
In ice-9/boot-9.scm:
2401: 11 [save-module-excursion #<procedure 27f2880 at ice-9/boot-9.scm:4045:3 ()>]
4050: 10 [#<procedure 27f2880 at ice-9/boot-9.scm:4045:3 ()>]
1724: 9 [%start-stack load-stack ...]
1729: 8 [#<procedure 2808c60 ()>]
In unknown file:
   ?: 7 [primitive-load "/gnu/store/6pzf2jhf9syyc02wbgl9mxma4wf2qxj2-preseq-1.0.2-guile-builder"]
In ice-9/eval.scm:
 387: 6 [eval # ()]
In srfi/srfi-1.scm:
 830: 5 [every1 #<procedure 2cb91e0 at /gnu/store/l1019wb5yzbar26cxxqrm88xkbn5gwv1-module-import/guix/build/gnu-build-system.scm:584:9 (expr)> ...]
In /gnu/store/l1019wb5yzbar26cxxqrm88xkbn5gwv1-module-import/guix/build/gnu-build-system.scm:
 588: 4 [#<procedure 2cb91e0 at /gnu/store/l1019wb5yzbar26cxxqrm88xkbn5gwv1-module-import/guix/build/gnu-build-system.scm:584:9 (expr)> #]
In ice-9/eval.scm:
 432: 3 [eval # #]
In srfi/srfi-1.scm:
 619: 2 [for-each #<procedure 2cf4de0 at ice-9/eval.scm:416:20 (a)> #]
In /gnu/store/l1019wb5yzbar26cxxqrm88xkbn5gwv1-module-import/guix/build/utils.scm:
 486: 1 [with-atomic-file-replacement "smithlab_cpp/SAM.cpp" ...]
In unknown file:
   ?: 0 [mkstemp! "smithlab_cpp/SAM.cpp.XXXXXX"]

ERROR: In procedure mkstemp!:
ERROR: In procedure mkstemp!: No such file or directory
builder for `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed with exit code 1
@ build-failed /gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv - 1 builder for `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed with exit code 1
guix build: error: build failed: build of `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed
--8<---------------cut here---------------end--------------->8---

      Mark

Re: [PATCH] Add preseq.

[Ricardo Wurmus]

> ERROR: In procedure mkstemp!:
> ERROR: In procedure mkstemp!: No such file or directory
> builder for `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed with exit code 1
> @ build-failed /gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv - 1 builder for `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed with exit code 1
> guix build: error: build failed: build of `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed

The problem was that the “enter-dir” and “use-samtools-headers” phases
were both added after “unpack”.  (Has the order in which phases are
added with ‘modify-phases’ changed?  When I built it locally back then
“use-samtools-headers” must have ended up after “enter-dir”.)

I just pushed a commit that explicitly moves “use-samtools-headers”
after the “enter-dir” phase, fixing this problem.

Thank you, Mark, for the notification.

~~ Ricardo

Re: [PATCH] Add preseq.

[Mark H Weaver]

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

>> ERROR: In procedure mkstemp!:
>> ERROR: In procedure mkstemp!: No such file or directory
>> builder for `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed with exit code 1
>> @ build-failed
>> /gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv - 1
>> builder for
>> `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv'
>> failed with exit code 1
>> guix build: error: build failed: build of `/gnu/store/2ll28ypms57h0k44f4mmclhw9dz3ccvm-preseq-1.0.2.drv' failed
>
> The problem was that the “enter-dir” and “use-samtools-headers” phases
> were both added after “unpack”.  (Has the order in which phases are
> added with ‘modify-phases’ changed?

No.  It's deterministic, and 'modify-phases' is in (guix build utils) so
it can't be changed without triggering a full rebuild.  The edits are
done in the order shown, as if it was imperative code.  For example:

  (modify-phases %standard-phases
    (add-after 'unpack 'A <phase-A>)
    (add-after 'unpack 'B <phase-B>))

expands into:

  (let* ((phases* %standard-phases)
         (phases* (alist-cons-after 'unpack 'A <phase-A> phases*))
         (phases* (alist-cons-after 'unpack 'B <phase-B> phases*)))
    phases*)

which is equivalent to:

  (alist-cons-after
   'unpack 'B <phase-B>
   (alist-cons-after
    'unpack 'A <phase-A>
    %standard-phases))

Since B is the last one added, it ends up after 'unpack' and before A.

> When I built it locally back then “use-samtools-headers” must have
> ended up after “enter-dir”.)

I don't see how that could have happened.  Maybe you made some changes
after your last test?  Anyway, if 'use-samtools-headers' must come after
'enter-dir' then it's surely better to make that explicit.

> I just pushed a commit that explicitly moves “use-samtools-headers”
> after the “enter-dir” phase, fixing this problem.

Thank you!

    Mark

Re: [PATCH] Add preseq.

[Ricardo Wurmus]

Mark H Weaver <mhw@netris.org> writes:

> No.  It's deterministic, and 'modify-phases' is in (guix build utils) so
> it can't be changed without triggering a full rebuild.  The edits are
> done in the order shown, as if it was imperative code.  For example:

Thank you for confirming the behaviour.

>> When I built it locally back then “use-samtools-headers” must have
>> ended up after “enter-dir”.)
>
> I don't see how that could have happened.  Maybe you made some changes
> after your last test?  Anyway, if 'use-samtools-headers' must come after
> 'enter-dir' then it's surely better to make that explicit.

In that case it must have been that I made a change (reordering the
phases) and forgot to build preseq afterward.  My apologies for the
noise!

~~ Ricardo

Re: [PATCH] Add preseq.

[Ricardo Wurmus]

> Attached is a new version that includes support for BAM files, but
> without using the bundled version of samtools.  Two patches were
> necessary that I have submitted upstream.
>
> I'm still testing this with a user, and I'm waiting for upstream to
> comment on the patches, so I'm not in a hurry to push this.

Upstream merged the patches, but there's no new release yet.  See
https://github.com/smithlabcode/preseq/pull/15.

It seems to work fine.

~~ Ricardo