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
