| Message ID | 87eg4cyni4.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me |
|---|---|
| State | New |
| Headers | show |
On 09/23/2016 01:15 AM, Marius Bakke wrote: > Ben Woodcroft <b.woodcroft@uq.edu.au> writes: > >>> Subject: [PATCH 1/3] gnu: python-pysam: Update to 0.9.1.4. >> I'm not sure whether this is a product of the upgrade or not, but I >> notice this in the build log. I think it is harmless though, WDYT? >> >> starting phase `validate-runpath' >> validating RUNPATH of 10 binaries in >> "/gnu/store/bpiq3lm6b1kpf54i1vj2dl09ff293wic-python-pysam-0.9.1.4/lib"... >> /gnu/store/bpiq3lm6b1kpf54i1vj2dl09ff293wic-python-pysam-0.9.1.4/lib/python3.4/site-packages/pysam-0.9.1.4-py3.4-linux-x86_64.egg/pysam/libchtslib.cpython-34m.so: >> warning: RUNPATH contains bogus entries: ("pysam" "." >> "build/lib.linux-x86_64-3.4/pysam") > I don't see this in the previous version, so it is a regression. > However, it should be mostly harmless. Readelf reports (when compiled > with external htslib, see below): > > 0x000000000000001d (RUNPATH) Library runpath: [/gnu/store/m4gc2wx4q9if1vrhgclpspdil7rqsn21-python-3.4.3/lib:/gnu/store/ba22myqvxccwmmjwwq665rc43hanycxy-htslib-1.3.1/lib:build/lib.linux-x86_64-3.4/pysam:$ORIGIN:/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib:/gnu/store/xl19qrfzga52vrvp4ncccwjlnrjqwj95-ncurses-6.0/lib:/gnu/store/5992iq1v7arqa14ym3di58n4la0893nv-zlib-1.2.8/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/../../..] > > Compared to the runpath of the same file currently in Guix: > > 0x000000000000001d (RUNPATH) Library runpath: [/gnu/store/m4gc2wx4q9if1vrhgclpspdil7rqsn21-python-3.4.3/lib:/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib:/gnu/store/xl19qrfzga52vrvp4ncccwjlnrjqwj95-ncurses-6.0/lib:/gnu/store/5992iq1v7arqa14ym3di58n4la0893nv-zlib-1.2.8/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/../../..] > > If a folder named "$CWD/build/lib.linux-x86_64-3.4/pysam exists, it > could potentially allow for code injection, which is troubling. > > I opened an issue on their tracker, but don't think it's worth holding > the patch: https://github.com/pysam-developers/pysam/issues/347 Thanks, I agree. > >> Also, I notice that pysam bundles htslib, bcftools and samtools C code. >> Hopefully it should be straightforward enough to remove htslib as there >> are install instructions, I'm not sure about the other two. This >> shouldn't block the patch here, but would you mind taking a look? >> http://pysam.readthedocs.io/en/latest/installation.html#installation > I had a go at this, and also enabled tests since I was reading the build > system anyway. Samtools and bcftools does not seem possible to un-bundle > at this time, but htslib was straightforward. OK. I don't think it needs to be propagated though, right? Also, would you mind separating the change to modify-phases syntax and unbundling of htslib into two patches please? Other than that this whole series LGTM. Sorry, I keep asking one more thing.. ben
From ab4f0a5174554a7f2b7b243b5488654de7d81ac1 Mon Sep 17 00:00:00 2001 From: Marius Bakke <mbakke@fastmail.com> Date: Thu, 22 Sep 2016 14:11:59 +0100 Subject: [PATCH 6/6] gnu: python-pysam: Enable tests. * gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from PyPi to source archive due to missing test data. [arguments]: Add check phase after install. [native-inputs]: Add python-nose, samtools and bcftools. --- gnu/packages/bioinformatics.scm | 33 ++++++++++++++++++++++++++++----- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index edfb943..abbe601 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1353,18 +1353,21 @@ multiple sequence alignments.") (version "0.9.1.4") (source (origin (method url-fetch) - (uri (pypi-uri "pysam" version)) + ;; Test data is missing on PyPi. + (uri (string-append + "https://github.com/pysam-developers/pysam/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn")) + "0y41ssbg6nvn2jgcbnrvkzblpjcwszaiv1rgyd8dwzjkrbfsgsmc")) (modules '((guix build utils))) (snippet ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. '(delete-file-recursively "htslib")))) (build-system python-build-system) (arguments - `(#:tests? #f ; tests are excluded in the manifest - #:phases + `(#:phases (modify-phases %standard-phases (add-before 'build 'set-flags (lambda* (#:key inputs #:allow-other-keys) @@ -1374,7 +1377,24 @@ multiple sequence alignments.") (assoc-ref inputs "htslib") "/lib")) (setenv "HTSLIB_INCLUDE_DIR" (string-append (assoc-ref inputs "htslib") "/include")) - (setenv "CFLAGS" "-D_CURSES_LIB=1")))))) + (setenv "CFLAGS" "-D_CURSES_LIB=1"))) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "PYTHONPATH" + (string-append + (getenv "PYTHONPATH") + ":" (assoc-ref outputs "out") + "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") 5) 3) + "/site-packages")) + ;; Step out of source dir so python does not import from CWD. + (chdir "tests") + (setenv "HOME" "/tmp") + (and (zero? (system* "make" "-C" "pysam_data")) + (zero? (system* "make" "-C" "cbcf_data")) + (zero? (system* "nosetests" "-v")))))))) (propagated-inputs `(("htslib" ,htslib))) (inputs @@ -1382,6 +1402,9 @@ multiple sequence alignments.") ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("samtools" ,samtools) + ("bcftools" ,bcftools) ("python-setuptools" ,python-setuptools))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") -- 2.10.0