commit 75fc8ae0f4380d790d71ba76da932b333b2a49f8 · pyrox.dev/nixpkgs

-27

pkgs/applications/science/biology/kent/kent-utils.patch

···

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       --- ./src/utils/bigWigCat/makefile.orig	2023-03-27 14:03:01.585896516 +0000

     

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       +++ ./src/utils/bigWigCat/makefile	2023-03-27 14:03:27.716180479 +0000

     

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       @@ -1,3 +1,4 @@

     

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        kentSrc = ../..

     

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        A = bigWigCat

     

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        include $(kentSrc)/inc/userApp.mk

     

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       +L += -lz

     

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       -
       

     

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       --- ./src/utils/pslLiftSubrangeBlat/makefile.orig	1970-01-01 00:00:01.000000000 +0000

     

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       +++ ./src/utils/pslLiftSubrangeBlat/makefile	2023-03-27 14:36:59.044600213 +0000

     

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       @@ -3,7 +3,7 @@

     

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        preMyLibs += ../../lib/$(MACHTYPE)/jkhgap.a

     

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        include $(kentSrc)/inc/userApp.mk

     

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        HG_INC += -I../../hg/inc

     

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       -L += $(MYSQLLIBS) -lm

     

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       +L += $(MYSQLLIBS) -lm -lz

     

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       -
        

     

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        test::

     

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        	cd tests && ${MAKE} test

     

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       --- ./src/utils/bigWigCorrelate/makefile.orig	2023-03-27 14:36:23.117545553 +0000

     

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       +++ ./src/utils/bigWigCorrelate/makefile	2023-03-27 14:36:33.854328176 +0000

     

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       @@ -1,3 +1,4 @@

     

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        kentSrc = ../..

     

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        A = bigWigCorrelate

     

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        include $(kentSrc)/inc/userApp.mk

     

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       -
       +L += -lz

+7 -7

pkgs/development/perl-modules/Bio-BigFile/default.nix

···

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         # Only kent 335 works with Bio-BigFile, see

     

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         # - official documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#bigfile

     

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         # - one of the developer's answer: https://github.com/Ensembl/ensembl-vep/issues/1412

     

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         # KENT_SRC is needed for building BioBigfil

     

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         # BioBigfile needs the environment variable KENT_SRC to find kent

     

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         KENT_SRC = kent.overrideAttrs (old: rec {

     

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           pname = "kent";

     

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           version = "335";

     
···

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             sha256 = "1455dwzpaq4hyhcqj3fpwgq5a39kp46qarfbr6ms6l2lz583r083";

     

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           };

     

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       -
           # The first patch is a custom fix  for linking error with zlib.

     

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           patches = [

     

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             # Fix  for linking error with zlib. Adding zlib as a dependency is not enough

     

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             ./kent-utils.patch

     

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             (fetchpatch {

     

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               url = "https://github.com/ucscGenomeBrowser/kent/commit/316e4fd40f53c96850128fd65097a42623d1e736.patch";

     

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               sha256 = "sha256-wr3NP5qoSonKz1TLKtQyrTPErCOk2gC1RimcX0tE7cM=";

     

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       -
             })];

     

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             # Vendoring upstream patch (not merged in uscsGenomeBrowser/kent)

     

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             ./kent-316e4fd40f53c96850128fd65097a42623d1e736.patch

     

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           ];

     

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         });

     

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···

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           openssl

     

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         ];

     

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       +
         # Ensure compatibility with GCC-11 (compilation fails if -Wno-format-security)

     

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         hardeningDisable = [ "format" ];

     

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         meta = with lib; {

     

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           homepage = "https://metacpan.org/dist/Bio-BigFile";

     

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           description = "Manipulate Jim Kent's BigWig and BigBed index files for genomic features";

     

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       -
           license = licenses.unfree;

     

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       +
           license = licenses.artistic2;

     

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           maintainers = with maintainers; [ apraga ];

     

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         };

     

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       }

+25

pkgs/development/perl-modules/Bio-BigFile/kent-316e4fd40f53c96850128fd65097a42623d1e736.patch

···

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       From 316e4fd40f53c96850128fd65097a42623d1e736 Mon Sep 17 00:00:00 2001

     

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       From: Marcel Bargull <marcel.bargull@udo.edu>

     

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       Date: Sat, 27 Mar 2021 16:23:34 +0100

     

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       Subject: [PATCH] Fix linking Clang 11 compiled objects

     

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       With Clang 11 htmlRecover from lib/htmshell.h is picked up as a

     

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       definition, not just declaration of the jmp_buf. As such both

     

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       lib/htmshell.c and hg/lib/cart.c export two symbols with the same name.

     

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       ---

     

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        src/inc/htmshell.h | 2 +-

     

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        1 file changed, 1 insertion(+), 1 deletion(-)

     

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       diff --git a/src/inc/htmshell.h b/src/inc/htmshell.h

     

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       index 9d85f45b936..dd586db761c 100644

     

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       --- a/src/inc/htmshell.h

     

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       +++ b/src/inc/htmshell.h

     

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       @@ -160,7 +160,7 @@ void htmlBadVar(char *varName);

     

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        void htmlImage(char *fileName, int width, int height);

     

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        /* Display centered image file. */

     

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       -jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */

     

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       +extern jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */

     

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        void htmlVaWarn(char *format, va_list args);

     

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        /* Write an error message.  (Generally you just call warn() or errAbort().