Re: [PATCH 3/3] gnu: Add khmer.

[Ben Woodcroft]

On 17/06/16 17:23, Leo Famulari wrote:
> On Fri, Jun 17, 2016 at 11:23:21AM +1000, Ben Woodcroft wrote:
> > +    (build-system python-build-system)
> > +    (arguments
> > +     `(#:phases
> > +       (modify-phases %standard-phases
> > +         (add-after 'unpack 'set-paths
> This phase deletes bundled libraries and then copies one of the
> libraries back in from another package (murmur-hash).
>
> Can khmer refer to murmur-hash without it being bundled at all?

By changing the Makefile or similar so that it refers to a 'murmur-hash' 
shared library? Maybe, but I don't think SMHasher creates one of these.

If you mean just referring to the code as it is in murmur-hash, then 
we'd have to change the Makefile so that it refers to that code. I 
figured copying the code in achieves the same thing with less effort on 
our part.

> > +           (lambda* (#:key inputs outputs #:allow-other-keys)
> > +             ;; Delete bundled libraries.
> > +             (delete-file-recursively "third-party/zlib")
> > +             (delete-file-recursively "third-party/bzip2")
> > +             ;; Replace bundled seqan.
> > +             (let* ((seqan-all "third-party/seqan")
> > +                    (seqan-include (string-append
> > +                                    seqan-all "/core/include/seqan")))
> > +               (delete-file-recursively seqan-all)
> > +               (mkdir-p seqan-include)
> > +               (rmdir seqan-include)
> Here it makes the directory seqan-include and then removes it. Should it
> be reversed? Would it be simpler to delete the directory and then use
> copy-recursively, which I don't think requires mkdir-p?

The issue is that there are other (unused) files in 'third-part/seqan' 
that aren't useful code, and I wanted to be sure to delete all the 
bundle before starting the build. How about the slightly simplified

+             (let* ((seqan-all "third-party/seqan")
+                    (seqan-include (string-append
+                                    seqan-all "/core/include")))
+               (delete-file-recursively seqan-all)
+               (mkdir-p seqan-include)
+               (copy-file (string-append (assoc-ref inputs "seqan")
+                                         "/include/seqan")
+                          (string-append seqan-include "/seqan")))

It would be better if I knew a way of copying directory into another 
directory, like an "install-directory".

> > +               (copy-file (string-append (assoc-ref inputs "seqan")
> > +                                         "/include/seqan")
> > +                          seqan-include))
> > +             ;; Replace bundled MurmurHash.
> > +             (let ((smhasher "third-party/smhasher/"))
> > +               (delete-file-recursively smhasher)
> > +               (mkdir smhasher)
> > +               (for-each
> > +                (lambda (file)
> > +                  (copy-file
> > +                   (string-append
> > +                    (assoc-ref inputs "murmur-hash") "/include/" file)
> > +                   (string-append smhasher file)))
> > +                (list "MurmurHash3.cpp" "MurmurHash3.h"))
> > +               (rename-file
> > +                (string-append smhasher "MurmurHash3.cpp")
> > +                (string-append smhasher "MurmurHash3.cc")))
> > +             (setenv "CC" "gcc")
> I think this variable setting should be in its own phase.

OK.

ben