Coder Social home page Coder Social logo

gbrowse-adaptors's People

Contributors

cjfields avatar drprofesq avatar ericenns avatar jwhsanger avatar keiranmraine avatar lstein avatar malcook avatar scottcain avatar

Stargazers

avatar avatar avatar avatar avatar avatar avatar avatar

Watchers

avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar

Forkers

gig77 jmarshall jwhsanger litswu iansealy nathanweeks

gbrowse-adaptors's Issues

Bio-BigFile - new versions of jksrc.zip are incompatible

The new versions of jksrc.zip start to use htslib and result in a failure to load the tbx functions:

Can't load '/nfs/users/nfs_k/kr2/tmp/Bio-BigFile-1.07/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so' for module Bio::DB::BigFile: /nfs/users/nfs_k/kr2/tmp/Bio-BigFile-1.07/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so: undefined symbol: tbx_readrec at /software/perl-5.16.3/lib/5.16.3/x86_64-linux-thread-multi/DynaLoader.pm line 190.

This oddity was that building under travis-ci with language set to 'c' works, but language 'perl' doesn't.

v334 of jksrc appears to be the last functioning version. Unfortunately they only keep a limited number of versions (the ones dating back to the release of BioBigFile are no longer present).

Missing test file on CPAN

GBrowse-Adaptors/Bio-SamTools/t/data/ex2.bam

Tests fail when run via cpanm:

~/.cpanm/work/1455272147.4882/Bio-SamTools-1.42/t/data/ex2.bam does not exist at t/01sam.t line 75.
t/01sam.t .. 
Dubious, test returned 2 (wstat 512, 0x200)
Failed 268/268 subtests 

Test Summary Report
-------------------
t/01sam.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 268 tests but ran 0.
Files=1, Tests=0,  0 wallclock secs ( 0.03 usr  0.01 sys +  0.36 cusr  0.07 csys =  0.47 CPU)
Result: FAIL
Failed 1/1 test programs. 0/0 subtests failed.

bedGraph2bigwig function

It would be nice if we have a function to transfer bedGraph to bigwig, what do you think about it?

can't build Bio-BigFile

Hello, not sure if anyone is active here but directed here by ucscGenomeBrowser/kent#51

Here is my problem,

I am trying to install Bio-BigFile-1.07 and consistently getting this error after ./Build

Building Bio-BigFile
cc -shared -O2 -L/usr/local/lib -fstack-protector -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o ~/kent/src/lib/x86_64/jkweb.a -lz -lssl
/usr/bin/ld: ~/kent/src/lib/x86_64/jkweb.a(bbiRead.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
~/kent/src/lib/x86_64/jkweb.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from lib/Bio/DB/BigFile.o at /software/perl/5.24.1/lib/5.20.2/ExtUtils/CBuilder/Base.pm line 323.

I updated the CFLAGS=-fPIC in kent/src/inc/common.mk and run make in kent/src/lib
Also followed the below instructions:

export MACHTYPE=x86_64
export PATH="~/bin/$MACHTYPE:$PATH

I also tried what is suggested here: http://seqanswers.com/forums/archive/index.php/t-70219.html

run make in Kent folders with following:
make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC

After this I'm finally passing ./Build but this time ./Build test fails,

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 29 tests but ran 0.
t/02.bigbed.t     (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
Files=5, Tests=0,  2 wallclock secs ( 0.07 usr  0.03 sys +  1.39 cusr  0.41 csys =  1.90 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.

It'd be great if you can help me about this.

Bio::DB::BigFile fails some unit tests

When installing Bio::DB::BigFile (as a dependency to PCAP-core) it fails some unit tests. Here is the build.log.

cpanm (App::cpanminus) 1.7042 on perl 5.018002 built for x86_64-linux-thread-multi-ld
Work directory is /home/godlovedc/.cpanm/work/1467299881.7444
You have make /usr/bin/make
You have LWP 6.15
You have /bin/tar: tar (GNU tar) 1.23
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Searching Bio::DB::BigFile () on cpanmetadb ...
--> Working on Bio::DB::BigFile
Fetching http://cpan.metacpan.org/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz
-> OK
Unpacking Bio-BigFile-1.07.tar.gz
Entering Bio-BigFile-1.07
Checking configure dependencies from META.json
Checking if you have Module::Build 0.38 ... Yes (0.4218)
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
Configuring Bio-BigFile-1.07
Running Build.PL
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-BigFile' version '1.07'
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have IO::String 0 ... Yes (1.08)
Checking if you have ExtUtils::CBuilder 0 ... Yes (0.280210)
Checking if you have Bio::Root::Version 1.005009001 ... Yes (1.006924)
Building and testing Bio-BigFile-1.07
Building Bio-BigFile
cc -I/usr/local/apps/ascatNgs/3.0.2/PCAP-core_git_repo/install_tmp/kent/src/inc -I/usr/local/Perl/5.18.2/lib/perl5/5.18.2/x86_64-linux-thread-multi-ld/CORE -DVERSION="1.07" -DXS_VERSION="1.07" -fPIC -Wno-format -Wformat=0 -DMACHTYPE_i686 -c -D_REENTRANT -D_GNU_SOURCE -fPIC -fno-strict-aliasing -pipe -fstack-protector -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o lib/Bio/DB/BigFile.o lib/Bio/DB/BigFile.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
cc -shared -O2 -L/usr/local/lib -fstack-protector -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o /usr/local/apps/ascatNgs/3.0.2/PCAP-core_git_repo/install_tmp/kent/src/lib/i686/jkweb.a -lz -lssl
# Test 20 got: "0.176919166116602751" (t/01.bigwig.t at line 89)
#    Expected: "0.176919166116602744"
#  t/01.bigwig.t line 89 is: ok ($extended_summary->sumData(1)/$extended_summary->validCount(1),$summary->[1]);
# Test 23 got: "0.0798449599229382158" (t/01.bigwig.t at line 94)
#    Expected: "0.079844959922938219"
#  t/01.bigwig.t line 94 is: ok($bin_sum->[300]->sumData/$bin_sum->[300]->validCount,$summary->[300]);
# Test 28 got: "0.0798449599229382158" (t/01.bigwig.t at line 101)
#    Expected: "0.079844959922938219"
#  t/01.bigwig.t line 101 is: ok($es_list->[300]{sumData}/$es_list->[300]{validCount},$summary->[300]);
t/01.bigwig.t .......
Failed 3/29 subtests
# Test 12 got: "1.00004166666666667" (t/02.bigbed.t at line 53)
#    Expected: "1.00004166666666672"
#  t/02.bigbed.t line 53 is: ok($es->[-2]{validCount}/(12_000_000/500),$summary->[-2]);
t/02.bigbed.t .......
Failed 1/15 subtests
t/03.bigwig_high.t .. ok
t/04.bigbed_high.t .. ok
t/05.bigwig_set.t ... ok

Test Summary Report
-------------------
t/01.bigwig.t     (Wstat: 0 Tests: 29 Failed: 3)
  Failed tests:  20, 23, 28
t/02.bigbed.t     (Wstat: 0 Tests: 15 Failed: 1)
  Failed test:  12
Files=5, Tests=135, 12 wallclock secs ( 0.07 usr  0.06 sys +  1.36 cusr  0.72 csys =  2.21 CPU)
Result: FAIL
Failed 2/5 test programs. 4/135 subtests failed.
-> FAIL Installing Bio::DB::BigFile failed. See /home/godlovedc/.cpanm/work/1467299881.7444/build.log for details. Retry with --force to force install it.

@keiranmraine thought it might be related to the way in which I installed nettle. For the record, I was unable to use a package manager to install nettle and I used this method.

umask 002
ASCAT_DIR=/usr/local/apps/ascatNgs/3.0.2
mkdir -p $ASCAT_DIR
cd $ASCAT_DIR
wget https://git.lysator.liu.se/nettle/nettle/repository/archive.tar.gz?ref=nettle_3.2_release_20160128 -O nettle.tar.gz
mkdir -p nettle.3.2
tar --strip-components 1 -C nettle.3.2 -zxf nettle.tar.gz
cd nettle.3.2
./.bootstrap
./configure --prefix=$ASCAT_DIR/nettle --disable-pic --disable-shared
make
make check
# all passed
make install
cd ..
rm -fr nettle.*

samtools/htslib 1.2 support

I managed to get samtools 1.2 support added in a samtools-1.2-cjf branch (this is based off the samtools-1.1 branch by @lstein ).

A few clunky things probably need to be cleaned up:

  1. The libraries seem to work best when compiled in directly (not using -L and -lbam -lhts). This also seems to address issues on Mac where clang/gcc will use libhts.dylib unless the full path to libhts.a is given.
  2. bam_lpileup and bam_sort functionality works if you also link in the object files in the samtools folder. Probably not optimal as users may remove those and only keep libbam.a and samtools. Maybe compiling them locally first to *.o in c_bin?

Tests are also fixed to address some API changes, in particular read1 returns 0 upon success and -1 upon failure.

Bio::DB::Bam::Alignment : $align->query->end < 0 !!!

It is possible to create an alignment from valid BAM data such that $align->query->end < 0 . The problem is that $query->end calls the samtools function bam_cigar2qlen() to get the total length and subtracts all clipping (hard and soft) at the end of the CIGAR. This is incorrect because bam_cigar2qlen() only accounts for soft clipping, so if there is hard clipping at the end as well then the return value is too small. If there is a lot of hard clipping then the result can be negative.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.