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Re: [PATCH] Add Blast+.
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From: |
Ricardo Wurmus |
|
Subject: |
Re: [PATCH] Add Blast+. |
|
Date: |
Tue, 23 Jun 2015 10:06:23 +0200 |
Hi Mark,
thank you for the review!
>> + `(;; There are three(!) tests for this massive library, and all fail
>> with
>> + ;; "unparsable timing stats".
>> + ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing
>> stats)
>> + ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable
>> timing stats)
>> + ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable
>> timing stats)
>> + #:tests? #f
>
> Just a guess, but maybe this is because you replaced "/bin/date" with
> "echo -n 0". How about replacing it with "date -d @0" instead?
I tried that but I still get the same problem. The test script is
generated from a template in common/check/check_make_unix.sh. We are
substituting "/var/tmp" for "/tmp" and the "(/usr)/bin" prefix, but this
should not have an impact on the functionality of the generated script.
I'm not sure why it's failing -- it works fine in "guix environment".
It's very time-consuming to recompile the whole thing until the tests
are reached.
> It would be great to get the tests working, even if we have to disable
> some of them. Otherwise we have no way of knowing that we're not
> distributing broken garbage :)
It's hard to know in this case even with the tests, because it's only
three tests and they seem hardly representative of the library.
>> +
>> + ;; rewrite "/var/tmp" in check script
>> + (substitute* "scripts/common/check/check_make_unix.sh"
>> + (("/var/tmp") (string-append (getcwd) "/build/build")))
>
> Or maybe just "/tmp" ?
Yes, that also works.
> All of these plus the ones for 'sh' could be combined into something
> like this: (untested)
[...]
This works great! Thank you.
>> + (("^ *PATH=.*") "")
>> + (("action=/bin/") "action=")
>> + (("export PATH") "echo -n 0"))
>
> Why "echo -n 0" here? Maybe ":" would be better? It is a no-op
> built-in command in Bourne shell.
Yes, this works. I needed to replace it with a no-op because "export
PATH" is also found in the middle of a long chain of commands, so
replacing it with the empty string results in a syntax error.
> Is everything in here really in the public domain? I'd guess that in
> order to make this true, you'd need to remove bzip2 and zlib in a
> snippet, and even then I'd doubtful :)
I've moved the code to remove the bundled stuff to a snippet.
The NCBI code was released into the public domain. However, it appears
that some third-party headers and some build scripts are under a
different license:
* Expat:
* ncbi-blast-2.2.30+-src/c++/include/util/bitset/
* ncbi-blast-2.2.30+-src/c++/src/html/ncbi_menu*.js
* Boost license:
* ncbi-blast-2.2.30+-src/c++/include/util/impl/floating_point_comparison.hpp
* LGPL 2+:
* ncbi-blast-2.2.30+-src/c++/include/dbapi/driver/odbc/unix_odbc/
* ASL 2.0:
* ncbi-blast-2.2.30+-src/c++/src/corelib/teamcity_*
I could not find mention of any other licenses. Is this correct, then:
;; Most of the sources are in the public domain, with the following
exceptions:
;; ...(the above list)...
(license (list license:public-domain
license:expat
license:boost1.0
license:lgpl2.0+
license:asl2.0))
What do you think?
~~ Ricardo
>From 8d131f66ba0378738e5b837f78c411edb241d35a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Tue, 16 Jun 2015 16:24:24 +0200
Subject: [PATCH] gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+): New variable.
---
gnu/packages/bioinformatics.scm | 155 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 155 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3defac8..4603329 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -31,6 +31,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages cpio)
#:use-module (gnu packages file)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
@@ -258,6 +259,160 @@ into separate processes; and more.")
(inputs
`(("python2-numpy" ,python2-numpy)))))
+(define-public blast+
+ (package
+ (name "blast+")
+ (version "2.2.30")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/";
+ version "/ncbi-blast-" version "+-src.tar.gz"))
+ (sha256
+ (base32
+ "0h0fj5cpx6zpfwixgx5f5xbr4rn3cnai0x3j7grrg50vr18jvxr6"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove bundled bzip2 and zlib
+ (delete-file-recursively "c++/src/util/compress/bzip2")
+ (delete-file-recursively "c++/src/util/compress/zlib")
+ (substitute* "c++/src/util/compress/Makefile.in"
+ (("bzip2 zlib api") "api"))
+ ;; Remove useless msbuild directory
+ (delete-file-recursively
+ "c++/src/build-system/project_tree_builder/msbuild")))))
+ (build-system gnu-build-system)
+ (arguments
+ `(;; There are three(!) tests for this massive library, and all fail with
+ ;; "unparsable timing stats".
+ ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing
stats)
+ ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing
stats)
+ ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable
timing stats)
+ #:tests? #f
+ #:out-of-source? #t
+ #:parallel-build? #f ; not supported
+ #:phases
+ (modify-phases %standard-phases
+ (add-before
+ 'configure 'set-HOME
+ ;; $HOME needs to be set at some point during the configure phase
+ (lambda _ (setenv "HOME" "/tmp") #t))
+ (add-after
+ 'unpack 'enter-dir
+ (lambda _ (chdir "c++") #t))
+ (add-after
+ 'enter-dir 'fix-build-system
+ (lambda _
+ (define (which* cmd)
+ (cond ((string=? cmd "date")
+ ;; make call to "date" deterministic
+ "date -d @0")
+ ((which cmd)
+ => identity)
+ (else
+ (format (current-error-port)
+ "WARNING: Unable to find absolute path for ~s~%"
+ cmd)
+ #f)))
+
+ ;; Proceed even though the weird build system says that generated
+ ;; files are out of date
+ (setenv "NCBICXX_RECONF_POLICY" "warn")
+
+ ;; Rewrite hardcoded paths to various tools
+ (substitute* (append (find-files "scripts/common/check" "\\.sh$")
+ '("scripts/common/impl/if_diff.sh"
+ "scripts/common/impl/run_with_lock.sh"
+
"src/build-system/Makefile.configurables.real"
+ "src/build-system/Makefile.in.top"
+ "src/build-system/Makefile.meta.gmake=no"
+ "src/build-system/Makefile.meta.in"
+ "src/build-system/Makefile.meta_l"
+ "src/build-system/Makefile.meta_p"
+ "src/build-system/Makefile.meta_r"
+ "src/build-system/Makefile.mk.in"
+ "src/build-system/Makefile.requirements"
+
"src/build-system/Makefile.rules_with_autodep.in"
+ "src/build-system/configure"
+ "src/build-system/configure.ac"))
+ (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
+ (or (which* cmd) all)))
+
+ ;; Some of the files we're patching are
+ ;; ISO-8859-1-encoded, so choose it as the default
+ ;; encoding so the byte encoding is preserved.
+ (with-fluids ((%default-port-encoding #f))
+ (substitute* (find-files "src/build-system" "^config.*")
+ (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
+ (("^PATH=.*") "")))
+
+ ;; rewrite "/var/tmp" in check script
+ (substitute* "scripts/common/check/check_make_unix.sh"
+ (("/var/tmp") "/tmp"))
+
+ ;; do not reset PATH
+ (substitute* (find-files "scripts/common/impl/" "\\.sh$")
+ (("^ *PATH=.*") "")
+ (("action=/bin/") "action=")
+ (("export PATH") ":"))
+ #t))
+ (replace
+ 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (lib (string-append (assoc-ref outputs "lib") "/lib"))
+ (include (string-append (assoc-ref outputs "include")
+ "/include/ncbi-tools++")))
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (zero? (system* "./configure.orig"
+ (string-append "--with-build-root=" (getcwd)
"/build")
+ (string-append "--prefix=" out)
+ (string-append "--libdir=" lib)
+ (string-append "--includedir=" include)
+ (string-append "--with-bz2="
+ (assoc-ref inputs "bzip2"))
+ (string-append "--with-z="
+ (assoc-ref inputs "zlib"))
+ ;; Each library is built twice by default, once
+ ;; with "-static" in its name, and again
+ ;; without.
+ "--without-static"
+ "--with-dll"))))))))
+ (outputs '("out" ; 19 MB
+ "lib" ; 203 MB
+ "include")) ; 32 MB
+ (inputs
+ `(("bzip2" ,bzip2)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("cpio" ,cpio)))
+ (home-page "http://blast.ncbi.nlm.nih.gov";)
+ (synopsis "Basic local alignment search tool")
+ (description
+ "BLAST is a popular method of performing a DNA or protein sequence
+similarity search, using heuristics to produce results quickly. It also
+calculates an “expect value” that estimates how many matches would have
+occurred at a given score by chance, which can aid a user in judging how much
+confidence to have in an alignment.")
+ ;; Most of the sources are in the public domain, with the following
+ ;; exceptions:
+ ;; * Expat:
+ ;; * ./c++/include/util/bitset/
+ ;; * ./c++/src/html/ncbi_menu*.js
+ ;; * Boost license:
+ ;; * ./c++/include/util/impl/floating_point_comparison.hpp
+ ;; * LGPL 2+:
+ ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
+ ;; * ASL 2.0:
+ ;; * ./c++/src/corelib/teamcity_*
+ (license (list license:public-domain
+ license:expat
+ license:boost1.0
+ license:lgpl2.0+
+ license:asl2.0))))
+
(define-public bowtie
(package
(name "bowtie")
--
2.1.0