Ubuntu14 installation error

[yichao-cai]

Hi,

I've trying to install wiggletools on my desktop. Followed the installation instructions, I installed all pre-requisite package but still can't install wiggletools.

This is the output when I run sudo make

mkdir -p bin
cd src; make -e
make[1]: Entering directory `/home/yichao/Documents/software/WiggleTools/src'
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wiggleIterator.c -o wiggleIterator.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wigReader.c -o wigReader.o
wigReader.c: In function ‘WiggleReaderSeek’:
wigReader.c:216:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o
bigWiggleReader.c: In function ‘BigWiggleReaderSeek’:
bigWiggleReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c multiplexer.c -o multiplexer.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c reducers.c -o reducers.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bedReader.c -o bedReader.o
bedReader.c: In function ‘BedReaderSeek’:
bedReader.c:95:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bigBedReader.c -o bigBedReader.o
bigBedReader.c: In function ‘BigBedReaderSeek’:
bigBedReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bamReader.c -o bamReader.o
bamReader.c: In function ‘BamReaderSeek’:
bamReader.c:201:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c apply.c -o apply.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c commandParser.c -o commandParser.o
commandParser.c: In function ‘parseFile’:
commandParser.c:872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(buffer, 1, length, file);
       ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wigWriter.c -o wigWriter.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c statistics.c -o statistics.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c unaryOps.c -o unaryOps.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c multiSet.c -o multiSet.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c setComparisons.c -o setComparisons.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bufferedReader.c -o bufferedReader.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c vcfReader.c -o vcfReader.o
vcfReader.c: In function ‘VcfReaderSeek’:
vcfReader.c:70:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bcfReader.c -o bcfReader.o
bcfReader.c: In function ‘downloadBCFFile’:
bcfReader.c:53:3: warning: passing argument 2 of ‘pushValuesToBuffer’ discards ‘const’ qualifier from pointer target type [enabled by default]
   if (pushValuesToBuffer(data->bufferedReaderData, bcf_hdr_id2name(data->bcf_header, vcf_line->rid), vcf_line->pos+1, vcf_line->pos+2, 1))
   ^
In file included from bcfReader.c:19:0:
bufferedReader.h:26:6: note: expected ‘char *’ but argument is of type ‘const char *’
 bool pushValuesToBuffer(BufferedReaderData * data, char * chrom, int start, int finish, double value);
      ^
bcfReader.c: In function ‘BcfReaderSeek’:
bcfReader.c:94:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c plots.c -o plots.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c mWigWriter.c -o mWigWriter.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c recycleBin.c -o recycleBin.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c fib.c -o fib.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c samReader.c -o samReader.o
samReader.c: In function ‘SamReaderSeek’:
samReader.c:186:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
mkdir -p ../lib
ar rcs ../lib/libwiggletools.a *.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wiggletools.c -o wiggletools.o
mkdir -p ../bin
cc -g -Wall -O3 -std=gnu99 -L../lib wiggletools.c -lwiggletools -lBigWig -lcurl -lhts -lgsl  -lgslcblas -lz -lpthread -lm -o ../bin/wiggletools 
make[1]: Leaving directory `/home/yichao/Documents/software/WiggleTools/src'
cd python/wiggletools; make
make[1]: Entering directory `/home/yichao/Documents/software/WiggleTools/python/wiggletools'
mkdir -p ../../bin
cp [^_]*.py *.sh ../../bin
make[1]: Leaving directory `/home/yichao/Documents/software/WiggleTools/python/wiggletools'
chmod 755 bin/*

When I run sudo make test, there is an error:

cd test; python2.7 test.py
Testing: ../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig
../bin/wiggletools: error while loading shared libraries: libBigWig.so: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "test.py", line 22, in <module>
    assert test('../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig') == 1
AssertionError
make: *** [tests] Error 1

Can you help me figure out what might went wrong? Thank you so much!

[obenno]

Hi,

I think this may be caused by your libBigwig, you sure it was well installed?

Obenno

On Fri, Jun 9, 2017 at 11:29 AM, YichaoCaiDBS notifications@github.com wrote:

Hi,

I've trying to install wiggletools on my desktop. Followed the installation instructions, I installed all pre-requisite package but still can't install wiggletools.

This is the output when I run sudo make

mkdir -p bin cd src; make -e make[1]: Entering directory /home/yichao/Documents/software/WiggleTools/src' cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wiggleIterator.c -o wiggleIterator.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wigReader.c -o wigReader.o wigReader.c: In function ‘WiggleReaderSeek’: wigReader.c:216:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o bigWiggleReader.c: In function ‘BigWiggleReaderSeek’: bigWiggleReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c multiplexer.c -o multiplexer.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c reducers.c -o reducers.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bedReader.c -o bedReader.o bedReader.c: In function ‘BedReaderSeek’: bedReader.c:95:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bigBedReader.c -o bigBedReader.o bigBedReader.c: In function ‘BigBedReaderSeek’: bigBedReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bamReader.c -o bamReader.o bamReader.c: In function ‘BamReaderSeek’: bamReader.c:201:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c apply.c -o apply.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c commandParser.c -o commandParser.o commandParser.c: In function ‘parseFile’: commandParser.c:872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer, 1, length, file); ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wigWriter.c -o wigWriter.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c statistics.c -o statistics.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c unaryOps.c -o unaryOps.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c multiSet.c -o multiSet.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c setComparisons.c -o setComparisons.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bufferedReader.c -o bufferedReader.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c vcfReader.c -o vcfReader.o vcfReader.c: In function ‘VcfReaderSeek’: vcfReader.c:70:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bcfReader.c -o bcfReader.o bcfReader.c: In function ‘downloadBCFFile’: bcfReader.c:53:3: warning: passing argument 2 of ‘pushValuesToBuffer’ discards ‘const’ qualifier from pointer target type [enabled by default] if (pushValuesToBuffer(data->bufferedReaderData, bcf_hdr_id2name(data->bcf_header, vcf_line->rid), vcf_line->pos+1, vcf_line->pos+2, 1)) ^ In file included from bcfReader.c:19:0: bufferedReader.h:26:6: note: expected ‘char *’ but argument is of type ‘const char *’ bool pushValuesToBuffer(BufferedReaderData * data, char * chrom, int start, int finish, double value); ^ bcfReader.c: In function ‘BcfReaderSeek’: bcfReader.c:94:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c plots.c -o plots.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c mWigWriter.c -o mWigWriter.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c recycleBin.c -o recycleBin.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c fib.c -o fib.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c samReader.c -o samReader.o samReader.c: In function ‘SamReaderSeek’: samReader.c:186:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ mkdir -p ../lib ar rcs ../lib/libwiggletools.a *.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wiggletools.c -o wiggletools.o mkdir -p ../bin cc -g -Wall -O3 -std=gnu99 -L../lib wiggletools.c -lwiggletools -lBigWig -lcurl -lhts -lgsl -lgslcblas -lz -lpthread -lm -o ../bin/wiggletools make[1]: Leaving directory/home/yichao/Documents/software/WiggleTools/src' cd python/wiggletools; make make[1]: Entering directory /home/yichao/Documents/software/WiggleTools/python/wiggletools' mkdir -p ../../bin cp [^_]*.py *.sh ../../bin make[1]: Leaving directory/home/yichao/Documents/software/WiggleTools/python/wiggletools' chmod 755 bin/*

When I run sudo make test, there is an error:

cd test; python2.7 test.py Testing: ../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig ../bin/wiggletools: error while loading shared libraries: libBigWig.so: cannot open shared object file: No such file or directory Traceback (most recent call last): File "test.py", line 22, in assert test('../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig') == 1 AssertionError make: *** [tests] Error 1

Can you help me figure out what might went wrong? Thank you so much!

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[yichao-cai]

I delete the libBigwig folder and install again. The output of the make install is :

cc -I. -g -Wall -O3 -Wsign-compare  -c -o io.o io.c
cc -I. -g -Wall -O3 -Wsign-compare  -c -o bwValues.o bwValues.c
cc -I. -g -Wall -O3 -Wsign-compare  -c -o bwRead.o bwRead.c
cc -I. -g -Wall -O3 -Wsign-compare  -c -o bwStats.o bwStats.c
cc -I. -g -Wall -O3 -Wsign-compare  -c -o bwWrite.o bwWrite.c
ar -rcs libBigWig.a io.o bwValues.o bwRead.o bwStats.o bwWrite.o
ranlib libBigWig.a
cc -I. -g -Wall -O3 -Wsign-compare  -fpic -c -o io.pico io.c
cc -I. -g -Wall -O3 -Wsign-compare  -fpic -c -o bwValues.pico bwValues.c
cc -I. -g -Wall -O3 -Wsign-compare  -fpic -c -o bwRead.pico bwRead.c
cc -I. -g -Wall -O3 -Wsign-compare  -fpic -c -o bwStats.pico bwStats.c
cc -I. -g -Wall -O3 -Wsign-compare  -fpic -c -o bwWrite.pico bwWrite.c
cc -shared  -o libBigWig.so io.pico bwValues.pico bwRead.pico bwStats.pico bwWrite.pico  -lcurl -lm -lz
install -d /usr/local/lib /usr/local/include
install libBigWig.a /usr/local/lib
install libBigWig.so /usr/local/lib
install *.h /usr/local/include

Still, the same error when I run make test in WiggleTools.

[obenno]

Could you print output of:

echo $LD_LIBRARY_PATH ?

On Fri, Jun 9, 2017 at 12:34 PM, YichaoCaiDBS notifications@github.com wrote:

I delete the libBigwig folder and install again. The output of the make install is :

cc -I. -g -Wall -O3 -Wsign-compare -c -o io.o io.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwValues.o bwValues.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwRead.o bwRead.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwStats.o bwStats.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwWrite.o bwWrite.c ar -rcs libBigWig.a io.o bwValues.o bwRead.o bwStats.o bwWrite.o ranlib libBigWig.a cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o io.pico io.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwValues.pico bwValues.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwRead.pico bwRead.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwStats.pico bwStats.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwWrite.pico bwWrite.c cc -shared -o libBigWig.so io.pico bwValues.pico bwRead.pico bwStats.pico bwWrite.pico -lcurl -lm -lz install -d /usr/local/lib /usr/local/include install libBigWig.a /usr/local/lib install libBigWig.so /usr/local/lib install *.h /usr/local/include

Still, the same error when I run make test in WiggleTools.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Ensembl/WiggleTools/issues/18#issuecomment-307292972, or mute the thread https://github.com/notifications/unsubscribe-auth/AF1oxGpC49lgyEbQwAc1WJdljX9JTvUrks5sCMtBgaJpZM4N03Rk .

[obenno]

If nothing out, pls add

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

to your .bashrc

On Fri, Jun 9, 2017 at 12:48 PM, zhixia xiao obennoname@gmail.com wrote:

Could you print output of:

echo $LD_LIBRARY_PATH ?

On Fri, Jun 9, 2017 at 12:34 PM, YichaoCaiDBS notifications@github.com wrote:

I delete the libBigwig folder and install again. The output of the make install is :

cc -I. -g -Wall -O3 -Wsign-compare -c -o io.o io.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwValues.o bwValues.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwRead.o bwRead.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwStats.o bwStats.c cc -I. -g -Wall -O3 -Wsign-compare -c -o bwWrite.o bwWrite.c ar -rcs libBigWig.a io.o bwValues.o bwRead.o bwStats.o bwWrite.o ranlib libBigWig.a cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o io.pico io.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwValues.pico bwValues.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwRead.pico bwRead.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwStats.pico bwStats.c cc -I. -g -Wall -O3 -Wsign-compare -fpic -c -o bwWrite.pico bwWrite.c cc -shared -o libBigWig.so io.pico bwValues.pico bwRead.pico bwStats.pico bwWrite.pico -lcurl -lm -lz install -d /usr/local/lib /usr/local/include install libBigWig.a /usr/local/lib install libBigWig.so /usr/local/lib install *.h /usr/local/include

Still, the same error when I run make test in WiggleTools.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Ensembl/WiggleTools/issues/18#issuecomment-307292972, or mute the thread https://github.com/notifications/unsubscribe-auth/AF1oxGpC49lgyEbQwAc1WJdljX9JTvUrks5sCMtBgaJpZM4N03Rk .

[yichao-cai]

Hi Obenno,

I tried your suggestion. The echo $LD_LIBRARY_PATH is indeed empty. After add it to my bashrc file and resource. I delete the WiggleTools and run the installation again.

Still the same error both during installation and make test

cd test; python2.7 test.py
Testing: ../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig
../bin/wiggletools: error while loading shared libraries: libBigWig.so: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "test.py", line 22, in <module>
    assert test('../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig') == 1
AssertionError
make: *** [tests] Error 1

[obenno]

Hi Yichao,

In previous installation,you got no error in the make step, right? Could you print the error info you got this time in make step?

If you use sudo make install to install libBigWig, then there should be libBigWig.so in /usr/local/lib, can you locate that file?

Obenno

On Fri, Jun 9, 2017 at 1:09 PM, YichaoCaiDBS notifications@github.com wrote:

Hi Obenno,

I tried your suggestion. The echo $LD_LIBRARY_PATH is indeed empty. After add it to my bashrc file and resource. I delete the WiggleTools and run the installation again.

Still the same error both during installation and make test

cd test; python2.7 test.py Testing: ../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig ../bin/wiggletools: error while loading shared libraries: libBigWig.so: cannot open shared object file: No such file or directory Traceback (most recent call last): File "test.py", line 22, in assert test('../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig') == 1 AssertionError make: *** [tests] Error 1

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[yichao-cai]

Hi Obenno,

The previous installation I got the same error as the one in the beginning of this thread.

mkdir -p bin
cd src; make -e
make[1]: Entering directory `/home/yichao/Documents/software/WiggleTools/src'
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wiggleIterator.c -o wiggleIterator.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wigReader.c -o wigReader.o
wigReader.c: In function ‘WiggleReaderSeek’:
wigReader.c:216:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o
bigWiggleReader.c: In function ‘BigWiggleReaderSeek’:
bigWiggleReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c multiplexer.c -o multiplexer.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c reducers.c -o reducers.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bedReader.c -o bedReader.o
bedReader.c: In function ‘BedReaderSeek’:
bedReader.c:95:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bigBedReader.c -o bigBedReader.o
bigBedReader.c: In function ‘BigBedReaderSeek’:
bigBedReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bamReader.c -o bamReader.o
bamReader.c: In function ‘BamReaderSeek’:
bamReader.c:201:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c apply.c -o apply.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c commandParser.c -o commandParser.o
commandParser.c: In function ‘parseFile’:
commandParser.c:872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(buffer, 1, length, file);
       ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wigWriter.c -o wigWriter.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c statistics.c -o statistics.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c unaryOps.c -o unaryOps.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c multiSet.c -o multiSet.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c setComparisons.c -o setComparisons.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bufferedReader.c -o bufferedReader.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c vcfReader.c -o vcfReader.o
vcfReader.c: In function ‘VcfReaderSeek’:
vcfReader.c:70:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c bcfReader.c -o bcfReader.o
bcfReader.c: In function ‘downloadBCFFile’:
bcfReader.c:53:3: warning: passing argument 2 of ‘pushValuesToBuffer’ discards ‘const’ qualifier from pointer target type [enabled by default]
   if (pushValuesToBuffer(data->bufferedReaderData, bcf_hdr_id2name(data->bcf_header, vcf_line->rid), vcf_line->pos+1, vcf_line->pos+2, 1))
   ^
In file included from bcfReader.c:19:0:
bufferedReader.h:26:6: note: expected ‘char *’ but argument is of type ‘const char *’
 bool pushValuesToBuffer(BufferedReaderData * data, char * chrom, int start, int finish, double value);
      ^
bcfReader.c: In function ‘BcfReaderSeek’:
bcfReader.c:94:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c plots.c -o plots.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c mWigWriter.c -o mWigWriter.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c recycleBin.c -o recycleBin.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c fib.c -o fib.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c samReader.c -o samReader.o
samReader.c: In function ‘SamReaderSeek’:
samReader.c:186:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^
mkdir -p ../lib
ar rcs ../lib/libwiggletools.a *.o
cc -g -Wall -O3 -std=gnu99  -D_PBGZF_USE -c wiggletools.c -o wiggletools.o
mkdir -p ../bin
cc -g -Wall -O3 -std=gnu99 -L../lib wiggletools.c -lwiggletools -lBigWig -lcurl -lhts -lgsl  -lgslcblas -lz -lpthread -lm -o ../bin/wiggletools 
make[1]: Leaving directory `/home/yichao/Documents/software/WiggleTools/src'
cd python/wiggletools; make
make[1]: Entering directory `/home/yichao/Documents/software/WiggleTools/python/wiggletools'
mkdir -p ../../bin
cp [^_]*.py *.sh ../../bin
make[1]: Leaving directory `/home/yichao/Documents/software/WiggleTools/python/wiggletools'
chmod 755 bin/*

I can locate the libBigWig.so in /usr/local/lib. But it seems that the test.py cant not find it.

Yichao

[obenno]

Hi Yichao,

If you got /usr/local/lib in your $LD_LIBRARY_PATH, and still get same error, then I've no clue now, hope someone else could help~ Sorry cannot help you fixing~

Obenno

On Fri, Jun 9, 2017 at 1:37 PM, YichaoCaiDBS notifications@github.com wrote:

Hi Obenno,

The previous installation I got the same error as the one in the beginning of this thread.

mkdir -p bin cd src; make -e make[1]: Entering directory /home/yichao/Documents/software/WiggleTools/src' cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wiggleIterator.c -o wiggleIterator.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wigReader.c -o wigReader.o wigReader.c: In function ‘WiggleReaderSeek’: wigReader.c:216:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o bigWiggleReader.c: In function ‘BigWiggleReaderSeek’: bigWiggleReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c multiplexer.c -o multiplexer.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c reducers.c -o reducers.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bedReader.c -o bedReader.o bedReader.c: In function ‘BedReaderSeek’: bedReader.c:95:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bigBedReader.c -o bigBedReader.o bigBedReader.c: In function ‘BigBedReaderSeek’: bigBedReader.c:98:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bamReader.c -o bamReader.o bamReader.c: In function ‘BamReaderSeek’: bamReader.c:201:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c apply.c -o apply.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c commandParser.c -o commandParser.o commandParser.c: In function ‘parseFile’: commandParser.c:872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer, 1, length, file); ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wigWriter.c -o wigWriter.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c statistics.c -o statistics.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c unaryOps.c -o unaryOps.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c multiSet.c -o multiSet.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c setComparisons.c -o setComparisons.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bufferedReader.c -o bufferedReader.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c vcfReader.c -o vcfReader.o vcfReader.c: In function ‘VcfReaderSeek’: vcfReader.c:70:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c bcfReader.c -o bcfReader.o bcfReader.c: In function ‘downloadBCFFile’: bcfReader.c:53:3: warning: passing argument 2 of ‘pushValuesToBuffer’ discards ‘const’ qualifier from pointer target type [enabled by default] if (pushValuesToBuffer(data->bufferedReaderData, bcf_hdr_id2name(data->bcf_header, vcf_line->rid), vcf_line->pos+1, vcf_line->pos+2, 1)) ^ In file included from bcfReader.c:19:0: bufferedReader.h:26:6: note: expected ‘char *’ but argument is of type ‘const char *’ bool pushValuesToBuffer(BufferedReaderData * data, char * chrom, int start, int finish, double value); ^ bcfReader.c: In function ‘BcfReaderSeek’: bcfReader.c:94:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c plots.c -o plots.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c mWigWriter.c -o mWigWriter.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c recycleBin.c -o recycleBin.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c fib.c -o fib.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c samReader.c -o samReader.o samReader.c: In function ‘SamReaderSeek’: samReader.c:186:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] data->chrom = chrom; ^ mkdir -p ../lib ar rcs ../lib/libwiggletools.a *.o cc -g -Wall -O3 -std=gnu99 -D_PBGZF_USE -c wiggletools.c -o wiggletools.o mkdir -p ../bin cc -g -Wall -O3 -std=gnu99 -L../lib wiggletools.c -lwiggletools -lBigWig -lcurl -lhts -lgsl -lgslcblas -lz -lpthread -lm -o ../bin/wiggletools make[1]: Leaving directory/home/yichao/Documents/software/WiggleTools/src' cd python/wiggletools; make make[1]: Entering directory /home/yichao/Documents/software/WiggleTools/python/wiggletools' mkdir -p ../../bin cp [^_]*.py *.sh ../../bin make[1]: Leaving directory/home/yichao/Documents/software/WiggleTools/python/wiggletools' chmod 755 bin/*

I can locate the libBigWig.so in /usr/local/lib. But it seems that the test.py cant not find it.

Yichao

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Ensembl/WiggleTools/issues/18#issuecomment-307300015, or mute the thread https://github.com/notifications/unsubscribe-auth/AF1oxLlKRncHZJ7HHvXCdqLTV_axdPquks5sCNoxgaJpZM4N03Rk .

[yichao-cai]

Hi Obenno

No worries. I will try to seek for others' advice. Thank you very much for your patience and help!

PS: After I add export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH to the .bashrc, I echo the path and the output is:

/usr/local/lib:

Is that correct?

Thanks, Yichao

[obenno]

Hi Yichao,

You're welcome.

It's correct, I'm using ubuntu 16.04, and it works well on my system. Will keep on following the thread~

Obenno

On Fri, Jun 9, 2017 at 2:14 PM, YichaoCaiDBS notifications@github.com wrote:

Hi Obenno

No worries. I will try to seek for others' advice. Thank you very much for your patience and help!

PS: After I add export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH to the .bashrc, I echo the path and the output is:

/usr/local/lib:

Is that correct?

Thanks, Yichao

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Ensembl/WiggleTools/issues/18#issuecomment-307304746, or mute the thread https://github.com/notifications/unsubscribe-auth/AF1oxPfhBUl0PfAIzdyUwpzuLOojuVAcks5sCOKtgaJpZM4N03Rk .

[dzerbino]

Good morning @YichaoCaiDBS and @obenno! Could you please check that there is a libBigWig.so file in /usr/local/lib?

• If not: failure in the installation procedure
• Else: failure in the linker.

[yichao-cai]

Hi @dzerbino

There is libBigWig.so in /usr/local/lib. If this is failure of the linker, how should I do to get it right?

Thank you ! Yichao

[dzerbino]

What are the permissions on the libBigWig.so file? I see you ran some sudos, do all users have permission to read and execute it?

[yichao-cai]

Hi @dzerbino ,

Sorry for late reply.

I've attached the output of ls under /usr/local/lib. Yes, the libBigWig.so is executable and readable by all users

-rwxr-xr-x  1 root root    390308 Jun  9 13:40 libBigWig.a
-rwxr-xr-x  1 root root    235210 Jun  9 13:40 libBigWig.so
-rw-r--r--  1 root root  19176040 Jun  9 11:17 libgsl.a
-rw-r--r--  1 root root   1758882 Jun  9 11:17 libgslcblas.a
-rwxr-xr-x  1 root root       949 Jun  9 11:17 libgslcblas.la
lrwxrwxrwx  1 root root        20 Jun  9 11:17 libgslcblas.so -> libgslcblas.so.0.0.0
lrwxrwxrwx  1 root root        20 Jun  9 11:17 libgslcblas.so.0 -> libgslcblas.so.0.0.0
-rwxr-xr-x  1 root root   1048362 Jun  9 11:17 libgslcblas.so.0.0.0
-rwxr-xr-x  1 root root       918 Jun  9 11:17 libgsl.la
lrwxrwxrwx  1 root root        16 Jun  9 11:17 libgsl.so -> libgsl.so.19.3.0
lrwxrwxrwx  1 root root        16 Jun  9 11:17 libgsl.so.19 -> libgsl.so.19.3.0
-rwxr-xr-x  1 root root  11353452 Jun  9 11:17 libgsl.so.19.3.0
-rw-r--r--  1 root root   5003244 Jun  9 11:02 libhts.a
lrwxrwxrwx  1 root root        27 Jun  9 11:16 libhts.so -> libhts.so.1.4.1-32-g5b9361d
-rw-r--r--  1 root root   3120855 Jun  9 11:02 libhts.so.1.4.1-32-g5b9361d
lrwxrwxrwx  1 root root        27 Jun  9 11:16 libhts.so.2 -> libhts.so.1.4.1-32-g5b9361d

Thank you!

[dzerbino]

Not exactly: libBigWig.so has 777 permissions, but it is a link to libhts.so.1.4.1-32-g5b9361d, which has 644 permissions. Could you please try chmod 755 /usr/local/lib/libhts.so.1.4.1-32-g5b9361d?

[yichao-cai]

Hi, I tried the suggestion and reinstall WiggleTools again. Again the make test returns me the same error.

Also, during installation there is one warning keeps occurring:

warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
  data->chrom = chrom;
              ^

And this warning occurs every time in the ReaderSeek function in Reader.c file.

[dzerbino]

Curious...

OK let's do this methodically. In the WiggleTools directory, when you type ldd bin/wiggletools, what do you get? This will allow us to understand what LD is doing at the moment.

[yichao-cai]

This is the output of ldd bin/wiggletools :

        linux-vdso.so.1 =>  (0x00007ffc3f30f000)
    libBigWig.so => /usr/local/lib/libBigWig.so (0x00007f0848327000)
    libhts.so.2 => /usr/local/lib/libhts.so.2 (0x00007f0848080000)
    libgsl.so.0 => /usr/lib/libgsl.so.0 (0x00007f0847c20000)
    libgslcblas.so.0 => /usr/local/lib/libgslcblas.so.0 (0x00007f08479e3000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f08477c5000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f08474bf000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f08470f7000)
    libcurl.so.4 => /usr/lib/x86_64-linux-gnu/libcurl.so.4 (0x00007f0846e90000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f0846c77000)
    libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f0846a67000)
    liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f0846845000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f0848536000)
    libidn.so.11 => /usr/lib/x86_64-linux-gnu/libidn.so.11 (0x00007f0846612000)
    librtmp.so.0 => /usr/lib/x86_64-linux-gnu/librtmp.so.0 (0x00007f08463f8000)
    libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007f0846199000)
    libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007f0845dbd000)
    libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007f0845b76000)
    liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2 (0x00007f0845967000)
    libldap_r-2.4.so.2 => /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 (0x00007f0845716000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f0845512000)
    libgnutls.so.26 => /usr/lib/x86_64-linux-gnu/libgnutls.so.26 (0x00007f0845253000)
    libgcrypt.so.11 => /lib/x86_64-linux-gnu/libgcrypt.so.11 (0x00007f0844fd3000)
    libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007f0844d08000)
    libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007f0844ad9000)
    libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007f08448d5000)
    libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007f08446ca000)
    libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f08444af000)
    libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007f0844294000)
    libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3 (0x00007f0844056000)
    libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007f0843e42000)
    libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007f0843c00000)
    libgpg-error.so.0 => /lib/x86_64-linux-gnu/libgpg-error.so.0 (0x00007f08439fb000)
    libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007f08437f7000)
    libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0 (0x00007f08435ee000)
    libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26 (0x00007f0843366000)
    libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8 (0x00007f08430c5000)
    libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4 (0x00007f0842e92000)
    libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18 (0x00007f0842c7d000)
    libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 (0x00007f0842a75000)
    libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0 (0x00007f084284c000)
    libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1 (0x00007f084263e000)
    libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5 (0x00007f08423f5000)
    libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f084213c000)
    libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007f0841f03000)

[dzerbino]

Wait, so it does find libBigWig.so!

What happens if you simply type ./bin/wiggletools? Then make test?

[yichao-cai]

Wow! I don't know what happened. But I've passed the test!

However, if I type wiggletools elsewhere, the computer can't found the programe. So, do I need to add the path path/to/bin/wiggletools to environment path?

Thank you!

Output of ./bin/wiggletools

WiggleTools

Copyright [1999-2017] EMBL-European Bioinformatics Institute
Development contact: Daniel Zerbino zerbino@ebi.ac.uk

Citation: Zerbino DR, Johnson N, Juettemann T, Wilder SP and Flicek PR: WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. Bioinformatics 2014 30:1008-1009.

This library parses wiggle files and executes various operations on them streaming through lazy evaluators.

Inputs:
    The program takes in Wig, BigWig, BedGraph, Bed, BigBed, Bam, VCF, and BCF files, which are distinguished thanks to their suffix (.wig, (.bw|.bigWig|.bigwig), .bg, .bed, .bb, .bam, .cram, .vcf, .bcf respectively).
    Note that wiggletools assumes that every bam file has an index .bai file next to it.

Outputs:
    The program outputs a wiggle file in stdout unless the output is squashed

Command line:
    wiggletools --help
    wiggletools program

Program grammar:
    program = (iterator) | do (iterator) | (extraction) | (statistic) | run (file)
    iterator = (in_filename) | (unary_operator) (iterator) | (binary_operator) (iterator) (iterator) | (reducer) (multiplex) | (setComparison) (multiplex_list) | print (output) (statistic)
    unary_operator = unit | coverage | write (output) | write_bg (ouput) | smooth (int) | abs | exp | ln | log (float) | pow (float) | offset (float) | scale (float) | gt (float) | lt (float) | default (float) | isZero | extend (int) | bin (int) | (statistic)
    output = (out_filename) | -
    in_filename = *.wig | *.bw | *.bed | *.bb | *.bg | *.bam | *.cram | *.vcf | *.bcf
    statistic = (statistic_function) (iterator) | ndpearson (multiplex) (multiplex)
    statistic_function = AUC | meanI | varI | minI | maxI | stddevI | CVI | energy (wavelength) | pearson (iterator)
    binary_operator = diff | ratio | overlaps | trim | noverlaps | nearest | apply (statistic) | fillIn
    reducer = cat | sum | product | mean | var | stddev | entropy | CV | median | min | max
    setComparison = ttest | ftest | wilcoxon
    multiplex_list = (multiplex) | (multiplex) : (multiplex_list)
    multiplex = (iterator_list) | map (unary_operator) (multiplex) | strict (multiplex)
    iterator_list = (iterator) | (iterator) : (iterator_list)
    extraction = profile (output) (int) (iterator) (iterator) | profiles (output) (int) (iterator) (iterator) | histogram (output) (width) (iterator_list) | mwrite (output) (multiplex) | mwrite_bg (output) (multiplex)
        | apply_paste (out_filename) (statistic) (bed_file) (iterator)

And then the test:

cd test; python2.7 test.py
Testing: ../bin/wiggletools do isZero diff fixedStep.bw variableStep.wig
Testing: ../bin/wiggletools diff fixedStep.bw variableStep.wig fixedStep.wig
Trailing tokens: the last tokens in your command were not read, check your syntax:
... fixedStep.wig
Testing: ../bin/wiggletools do isZero diff fixedStep.bw fixedStep.wig
Testing: ../bin/wiggletools do isZero offset -1 ratio variableStep.bw variableStep.wig
Testing: ../bin/wiggletools do isZero diff bam.bam pileup.bg
Testing: ../bin/wiggletools do isZero diff bam.bam cram.cram
[W::cram_populate_ref] Creating reference cache directory /home/yichao/.cache/hts-ref
This may become large; see the samtools(1) manual page REF_CACHE discussion
Testing: ../bin/wiggletools do isZero diff bam.bam sam.sam
Testing: cat sam.sam | ../bin/wiggletools do isZero diff bam.bam sam -
Testing: ../bin/wiggletools do isZero diff overlapping.bed overlapping.bb
Testing: ../bin/wiggletools do isZero diff variableStep.bw variableStep.wig
Testing: ../bin/wiggletools do isZero diff vcf.vcf bcf.bcf
Testing: ../bin/wiggletools do isZero diff sum fixedStep.bw fixedStep.bw : scale 2 fixedStep.bw
Testing: ../bin/wiggletools do isZero diff sum fixedStep.bw fixedStep.bw : sum fixedStep.bw fixedStep.bw 
Testing: ../bin/wiggletools do isZero diff ln fixedStep.bw sum map ln fixedStep.bw 
Testing: ../bin/wiggletools do isZero diff ln exp fixedStep.bw fixedStep.wig
Testing: ../bin/wiggletools do isZero diff pow 2 fixedStep.bw mult fixedStep.wig fixedStep.wig
Testing: ../bin/wiggletools do isZero diff lt 5 fixedStep.wig gt -5 scale -1 fixedStep.wig
Testing: ../bin/wiggletools apply_paste tmp/regional_means.txt meanI overlapping.bed fixedStep.wig
Testing: ../bin/wiggletools print tmp/pearson.txt pearson fixedStep.wig variableStep.wig
Testing: ../bin/wiggletools profiles tmp/profiles.txt 3 overlapping.bed fixedStep.wig
Testing: ../bin/wiggletools profile tmp/profile.txt 3 overlapping.bed fixedStep.wig
Testing: ../bin/wiggletools do isZero diff fixedStep.wig overlaps fixedStep.wig fixedStep.wig
Testing: ../bin/wiggletools write_bg tmp/nearest_overlapping.bg nearest variableStep.wig overlapping.bed
Testing: ../bin/wiggletools write_bg tmp/nearest_fixedStep.bg nearest variableStep.wig fixedStep.bw
Testing: ../bin/wiggletools print - minI fixedStep.wig
Testing: ../bin/wiggletools print - maxI fixedStep.wig
Testing: ../bin/wiggletools do isZero diff overlapping_coverage.wig coverage overlapping.bed
Testing: ../bin/wiggletools do isZero diff trim overlapping.bed variableStep.wig mult overlapping.bed variableStep.wig
Testing: ../bin/wiggletools run program.txt
Testing: diff tmp expected
All tests OK

[dzerbino]

Glad to hear it!

You can either copy ./bin/wiggletools into a directory of your path or add the directory it is contained in onto your path.

All the best,

Daniel