bedops installation error

[owwa]

Hi guys, could you please help to sort out a installation error for bedops? many thanks!

the platform is ubuntu 12.04 on a x86_64 machine;

I tried the following installation process, but it doesn't work:

svn checkout http://bedops.googlecode.com/svn/trunk/ bedops-read-only

cd bedops-read-only

make

----------------------------------------------------------------when i do make, i got the following errors:

touch applications/bed/sort-bed/src/.forcestatic

touch applications/bed/bedops/src/.forcestatic
touch applications/bed/closestfeats/src/.forcestatic
touch applications/bed/bedmap/src/.forcestatic
touch applications/bed/conversion/src/wig2bed/.forcestatic
touch applications/bed/bedextract/src/.forcestatic
test -s third-party/boost_1_46_1 || { bzcat third-party/boost_1_46_1.tar.bz2 | tar -x -C third-party; }
ln -sf boost_1_46_1 third-party/boost
test -s third-party/bzip2-1.0.6 || { bzcat third-party/bzip2-1.0.6.tar.bz2 | tar -x -C third-party; }
ln -sf bzip2-1.0.6 third-party/bzip2
test -s third-party/jansson-2.4 || { bzcat third-party/jansson-2.4.tar.bz2 | tar -x -C third-party; }
ln -sf jansson-2.4 third-party/jansson
test -s third-party/zlib-1.2.7 || { bzcat third-party/zlib-1.2.7.tar.bz2 | tar -x -C third-party; }
ln -sf zlib-1.2.7 third-party/zlib
make -C applications/bed/sort-bed/src
make[1]: Entering directory `/home/owwa/Downloads/methylations/bedops-read-only/applications/bed/sort-bed/src'
rm -rf .forcestatic
mkdir -p ../bin
mkdir -p objects
g++ -Wall -Wextra -ansi -pedantic -O3 -std=c++11 -s -c SortDetails.cpp -o objects/SortDetails.o -I../../../../interfaces/general-headers
cc1plus: error: unrecognized command line option ‘-std=c++11’
make[1]: *** [sortbuild] Error 1
make[1]: Leaving directory `/home/owwa/Downloads/methylations/bedops-read-only/applications/bed/sort-bed/src'
make: *** [sort_c] Error 2

[Alex Reynolds]

It sounds like you might be running an older version of GCC: the C and C++ compiler used to construct BEDOPS from code.

Can you run the following command and reply with the result?

$ gcc --version

This will tell us what version you're running and how to proceed.

Thanks,
Alex

[owwa]

gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


在 2013年7月5日星期五UTC+12下午6时10分02秒，Alex Reynolds写道：

[Alex Reynolds]

We recommend that you compile BEDOPS with GCC of version 4.7.2 or greater.

For Ubuntu, consider reviewing available GCC packages with 'apt-get', e.g.:

$ sudo apt-cache search gcc | grep gcc-4.7
gcc-4.7 - GNU C compiler
gcc-4.7-base - GCC, the GNU Compiler Collection (base package)
gcc-4.7-doc - Documentation for the GNU compilers (gcc, gobjc, g++)
...

Then:

$ sudo apt-get install gcc-4.7

Check that you have the correct GCC after installing:

$ gcc --version
gcc (Ubuntu/...)

Then continue with the BEDOPS build etc.

-Alex

[owwa]

it's strange!

after installation, the version is still the old one!

在 2013年7月5日星期五UTC+12下午6时45分01秒，Alex Reynolds写道：

[owwa]

~$ sudo apt-get install gcc-4.7
Reading package lists... Done
Building dependency tree      
Reading state information... Done
Note, selecting 'gcc-4.7-base' for regex 'gcc-4.7'
gcc-4.7-base is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

but

gcc --version

gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

在 2013年7月5日星期五UTC+12下午7时14分06秒，owwa写道：

[Alex Reynolds]

If you're having difficulties with getting GCC set up, you might also try Stack Overflow or Superuser as useful resources:

http://stackoverflow.com
http://superuser.com

-Alex

[owwa]

thanks Alex.

the following works for me:

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.7 g++-4.7
 

Also, don't forget to update-alternatives:

sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.6 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.6 
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.7 40 --slave /usr/bin/g++ g++ /usr/bin/g++-4.7 
sudo update-alternatives --config gcc

在 2013年7月5日星期五UTC+12下午7时21分12秒，Alex Reynolds写道：

[owwa]

i have update gcc to 4.7.3 and install the bedops, but when i run:

bam2bed < mybam459_34.bam > reads.bed

i still got the error:

*** glibc detected *** sort-bed: corrupted double-linked list: 0x0000000010753ca0 ***


在 2013年7月5日星期五UTC+12下午7时43分48秒，owwa写道：

[Alex Reynolds]

Perhaps you had some intermediate files left over. Please try:

$ make clean; make very-clean; make

Otherwise, if you want to make your reads available, we could try to replicate the issue on this end with your data as input. Dropbox is one place to share data publicly, or you could host the file somewhere else you prefer.

Feel free to contact off-list with links or other details.

-Alex

[Alex Reynolds]

(And: "make install" to ensure any old files are replaced in the ~/bin folder.)

[owwa]

I'm sorry. Alex.

the error is still here.

I'm sure that the sorted BAM file is ok. it's not so easy to upload because it's almost 1GB. I'd to go other way to do this transform. Thanks!

在 2013年7月5日星期五UTC+12下午8时12分46秒，Alex Reynolds写道：

[Alex Reynolds]

I'm sorry that you're still having trouble. Without being able to test sort-bed with your data, however, it's difficult for me to troubleshoot further. Dropbox offers 2 GB of free public storage, so your BAM file should be upload-able there, if you'd like me to do some testing. Or you could use another hosting service of your choice. Please contact me off-list if you decide to set this up.

Alternatively, you can pass the "--do-not-sort" option to the bam2bed script and it will skip applying sort-bed. I don't recommend this, as you may not get lexicographically-sorted BED output, which could cause problems with other BEDOPS tools (if you use them). If you don't need sorted BED data, then that might be an alternative.

Please let me know if you have any other questions.

Regards,
Alex

[owwa]

Hi Alex, thank you so much for your kind help!

I have made a smaller BAM file, could you please check it if you have time. thanks again.

Please see them at:
https://www.dropbox.com/s/q3i17gm6vdeeyyr/test.bam
https://www.dropbox.com/s/fzhtuv8ldggwuzf/test.bam.bai

在 2013年7月6日星期六UTC+12下午5时54分43秒，Alex Reynolds写道：