[bug#35207] [PATCH] Resurrect pplacer.

[bug#35207] [PATCH] Resurrect pplacer.

[Ricardo Wurmus]

Hi Guix,

this patch series adds pplacer, which had been removed due to its
dependency on the vulnerable OCaml 4.01.

-- 
Ricardo

[bug#35207] [PATCH 1/3] gnu: Add ocaml4.02-mcl.

[Ricardo Wurmus]

* gnu/packages/machine-learning.scm (ocaml4.02-mcl): New variable.
---
 gnu/packages/machine-learning.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 10aff22206..5b2786b61c 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -334,6 +334,9 @@ networks) based on simulation of (stochastic) flow in graphs.")
 algorithm.")
     (license license:gpl3)))
 
+(define-public ocaml4.02-mcl
+  (package-with-ocaml4.02 ocaml-mcl))
+
 (define-public randomjungle
   (package
     (name "randomjungle")
-- 
2.20.1

[bug#35207] [PATCH 2/3] gnu: Add ocaml4.02-gsl.

[Ricardo Wurmus]

* gnu/packages/ocaml.scm (ocaml4.02-gsl): New variable.
---
 gnu/packages/ocaml.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 7bebf3921b..bf5d39db6c 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -4824,6 +4824,28 @@ Atom.")
 the OCaml language.")
     (license license:gpl3+)))
 
+;; This is the last version that can be built with without ocaml-base, which
+;; cannot be built with OCaml 4.02.
+(define-public ocaml4.02-gsl
+  (package
+    (inherit (package-with-ocaml4.02 ocaml-gsl))
+    (version "1.19.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/mmottl/gsl-ocaml"
+                                  "/releases/download/v"
+                                  version "/gsl-ocaml-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
+    (build-system ocaml-build-system)
+    (inputs
+     `(("gsl" ,gsl)))
+    (arguments
+     `(#:ocaml ,ocaml-4.02
+       #:findlib ,ocaml4.02-findlib))
+    (propagated-inputs '())))
+
 (define-public cubicle
   (package
     (name "cubicle")
-- 
2.20.1

[bug#35207] [PATCH 3/3] gnu: Add pplacer.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
---
 gnu/packages/bioinformatics.scm | 151 ++++++++++++++++++++++++++++++++
 1 file changed, 151 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4cd032abd4..c073519dc3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14555,3 +14555,154 @@ overlapping paired-ended reads into (longer) consensus sequences.
 Additionally, the AdapterRemoval may be used to recover a consensus adapter
 sequence for paired-ended data, for which this information is not available.")
     (license license:gpl3+)))
+
+(define-public pplacer
+  (let ((commit "807f6f3"))
+    (package
+      (name "pplacer")
+      ;; The commit should be updated with each version change.
+      (version "1.1.alpha19")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/matsen/pplacer.git")
+               (commit (string-append "v" version))))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
+      (build-system ocaml-build-system)
+      (arguments
+       `(#:ocaml ,ocaml-4.02
+         #:findlib ,ocaml4.02-findlib
+         #:modules ((guix build ocaml-build-system)
+                    (guix build utils)
+                    (ice-9 ftw))
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (add-after 'unpack 'fix-build-with-ocaml-4.02
+             (lambda _
+               (substitute* "myocamlbuild.ml"
+                 (("let run_and_read" m)
+                  (string-append "
+let split s ch =
+  let x = ref [] in
+  let rec go s =
+    let pos = String.index s ch in
+    x := (String.before s pos)::!x;
+    go (String.after s (pos + 1))
+  in
+  try go s
+  with Not_found -> !x
+let split_nl s = split s '\\n'
+let before_space s =
+  try String.before s (String.index s ' ')
+  with Not_found -> s
+
+" m))
+                 (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m)
+                  (string-append "List.map before_space (split_nl & " m ")"))
+                 (("    blank_sep_strings &") "")
+                 (("      Lexing.from_string &") ""))
+               #t))
+           (add-after 'unpack 'replace-bundled-cddlib
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
+                      (local-dir "cddlib_guix"))
+                 (mkdir local-dir)
+                 (with-directory-excursion local-dir
+                   (invoke "tar" "xvf" cddlib-src))
+                 (let ((cddlib-src-folder
+                        (string-append local-dir "/"
+                                       (list-ref (scandir local-dir) 2)
+                                       "/lib-src")))
+                   (for-each make-file-writable (find-files "cdd_src" ".*"))
+                   (for-each
+                    (lambda (file)
+                      (copy-file file
+                                 (string-append "cdd_src/" (basename file))))
+                    (find-files cddlib-src-folder ".*[ch]$")))
+                 #t)))
+           (add-after 'unpack 'fix-makefile
+             (lambda _
+               ;; Remove system calls to 'git'.
+               (substitute* "Makefile"
+                 (("^DESCRIPT:=pplacer-.*")
+                  (string-append
+                   "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
+               (substitute* "myocamlbuild.ml"
+                 (("git describe --tags --long .*\\\" with")
+                  (string-append
+                   "echo -n v" ,version "-" ,commit "\" with")))
+               #t))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin")))
+                 (copy-recursively "bin" bin))
+               #t)))))
+      (inputs
+       `(("zlib" ,zlib "static")
+         ("gsl" ,gsl)
+         ("ocaml-ounit" ,ocaml4.02-ounit)
+         ("ocaml-batteries" ,ocaml4.02-batteries)
+         ("ocaml-camlzip" ,ocaml4.02-camlzip)
+         ("ocaml-csv" ,ocaml4.02-csv)
+         ("ocaml-sqlite3" ,ocaml4.02-sqlite3)
+         ("ocaml-xmlm" ,ocaml4.02-xmlm)
+         ("ocaml-mcl" ,ocaml4.02-mcl)
+         ("ocaml-gsl" ,ocaml4.02-gsl)))
+      (native-inputs
+       `(("cddlib-src" ,(package-source cddlib))
+         ("pkg-config" ,pkg-config)))
+      (propagated-inputs
+       `(("pplacer-scripts" ,pplacer-scripts)))
+      (synopsis "Phylogenetic placement of biological sequences")
+      (description
+       "Pplacer places query sequences on a fixed reference phylogenetic tree
+to maximize phylogenetic likelihood or posterior probability according to a
+reference alignment.  Pplacer is designed to be fast, to give useful
+information about uncertainty, and to offer advanced visualization and
+downstream analysis.")
+      (home-page "http://matsen.fhcrc.org/pplacer")
+      (license license:gpl3))))
+
+;; This package is installed alongside 'pplacer'.  It is a separate package so
+;; that it can use the python-build-system for the scripts that are
+;; distributed alongside the main OCaml binaries.
+(define pplacer-scripts
+  (package
+    (inherit pplacer)
+    (name "pplacer-scripts")
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-scripts-dir
+           (lambda _ (chdir "scripts") #t))
+         (replace 'check
+           (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
+         (add-after 'install 'wrap-executables
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (let ((path (string-append
+                            (assoc-ref inputs "hmmer") "/bin:"
+                            (assoc-ref inputs "infernal") "/bin")))
+                 (display path)
+                 (wrap-program (string-append bin "/refpkg_align.py")
+                   `("PATH" ":" prefix (,path))))
+               (let ((path (string-append
+                            (assoc-ref inputs "hmmer") "/bin")))
+                 (wrap-program (string-append bin "/hrefpkg_query.py")
+                   `("PATH" ":" prefix (,path)))))
+             #t)))))
+    (inputs
+     `(("infernal" ,infernal)
+       ("hmmer" ,hmmer)))
+    (propagated-inputs
+     `(("python-biopython" ,python2-biopython)
+       ("taxtastic" ,taxtastic)))
+    (synopsis "Pplacer Python scripts")))
-- 
2.20.1

[bug#35207] [PATCH] Resurrect pplacer.

[Julien Lepiller]

Le 9 avril 2019 15:00:02 GMT+02:00, Ricardo Wurmus <rekado@elephly.net> a écrit :
>Hi Guix,
>
>this patch series adds pplacer, which had been removed due to its
>dependency on the vulnerable OCaml 4.01.

We're going to have the same issue with ocaml-4.02, so I don't think we should add more dependents. I'd like to remove ocaml-4.02 but I'm a bit stuck because of bap right now.

What's the most recent version of ocaml pplacer can use?

[bug#35207] [PATCH] Resurrect pplacer.

[Ricardo Wurmus]

Julien Lepiller <julien@lepiller.eu> writes:

> What's the most recent version of ocaml pplacer can use?

It’s actually 4.01.  I don’t know how much effort it’s going to be to
make it work with the latest version.

-- 
Ricardo

[bug#35207] [PATCH] Resurrect pplacer.

[Ricardo Wurmus]

Ricardo Wurmus <rekado@elephly.net> writes:

> Julien Lepiller <julien@lepiller.eu> writes:
>
>> What's the most recent version of ocaml pplacer can use?
>
> It’s actually 4.01.  I don’t know how much effort it’s going to be to
> make it work with the latest version.

I gave patching pplacer a try, but in more recent versions of OCaml
strings are byte streams, so it’s quite a bit of work to figure out
where exactly to convert strings to byte streams and back again.

I’ll keep working on this for a while, but for now I’d like to get
pplacer resurrected with 4.02 first.

--
Ricardo

[bug#35207] [PATCH] Resurrect pplacer.

[Julien Lepiller]

Le 11 avril 2019 14:55:44 GMT+02:00, Ricardo Wurmus <rekado@elephly.net> a écrit :
>
>Ricardo Wurmus <rekado@elephly.net> writes:
>
>> Julien Lepiller <julien@lepiller.eu> writes:
>>
>>> What's the most recent version of ocaml pplacer can use?
>>
>> It’s actually 4.01.  I don’t know how much effort it’s going to be to
>> make it work with the latest version.
>
>I gave patching pplacer a try, but in more recent versions of OCaml
>strings are byte streams, so it’s quite a bit of work to figure out
>where exactly to convert strings to byte streams and back again.
>
>I’ll keep working on this for a while, but for now I’d like to get
>pplacer resurrected with 4.02 first.
>
>--
>Ricardo

Ok, I guess it's acceptable. I'll fully review your patches later today.

[bug#35207] [PATCH] Resurrect pplacer.

[Ricardo Wurmus]

Julien Lepiller <julien@lepiller.eu> writes:

> Le 11 avril 2019 14:55:44 GMT+02:00, Ricardo Wurmus <rekado@elephly.net> a écrit :
>>
>>Ricardo Wurmus <rekado@elephly.net> writes:
>>
>>> Julien Lepiller <julien@lepiller.eu> writes:
>>>
>>>> What's the most recent version of ocaml pplacer can use?
>>>
>>> It’s actually 4.01.  I don’t know how much effort it’s going to be to
>>> make it work with the latest version.
>>
>>I gave patching pplacer a try, but in more recent versions of OCaml
>>strings are byte streams, so it’s quite a bit of work to figure out
>>where exactly to convert strings to byte streams and back again.
>>
>>I’ll keep working on this for a while, but for now I’d like to get
>>pplacer resurrected with 4.02 first.
>>
>>--
>>Ricardo
>
> Ok, I guess it's acceptable. I'll fully review your patches later today.

Thanks for the offer, but it won’t be necessary after all.  I figured
out how to make it work with the latest OCaml.  I had to also patch
ocaml-mcl, but that seems okay.

New patches coming in a few minutes!

--
Ricardo

bug#35207: [PATCH] Resurrect pplacer.

[Ricardo Wurmus]

Ricardo Wurmus <rekado@elephly.net> writes:

> Julien Lepiller <julien@lepiller.eu> writes:
>
>> Le 11 avril 2019 14:55:44 GMT+02:00, Ricardo Wurmus <rekado@elephly.net> a écrit :
>>>
>>>Ricardo Wurmus <rekado@elephly.net> writes:
>>>
>>>> Julien Lepiller <julien@lepiller.eu> writes:
>>>>
>>>>> What's the most recent version of ocaml pplacer can use?
>>>>
>>>> It’s actually 4.01.  I don’t know how much effort it’s going to be to
>>>> make it work with the latest version.
>>>
>>>I gave patching pplacer a try, but in more recent versions of OCaml
>>>strings are byte streams, so it’s quite a bit of work to figure out
>>>where exactly to convert strings to byte streams and back again.
>>>
>>>I’ll keep working on this for a while, but for now I’d like to get
>>>pplacer resurrected with 4.02 first.
>>>
>>>--
>>>Ricardo
>>
>> Ok, I guess it's acceptable. I'll fully review your patches later today.
>
> Thanks for the offer, but it won’t be necessary after all.  I figured
> out how to make it work with the latest OCaml.  I had to also patch
> ocaml-mcl, but that seems okay.
>
> New patches coming in a few minutes!

I pushed the new patches to the “master” branch with commit 12327d7447.

-- 
Ricardo