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tophat installation problem

Dear friends,

While installing TopHat in my system I am getting the following errors. I have installed the boost library and also using --with boost option I am giving the path, but then also TopHat is not finding the boost library. I will be highly grateful to get any kind of ideas or help..

We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.
next-gen software-error
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updated by Ram Ram • written by skdutta2091 • skdutta2091

Why not just use the precompiled binaries?

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written by Devon Ryan Devon Ryan

I have successfully used the following configuration line to specify non-typical locations of Boost and TopHat 2.x:

./configure --with-bam=/path/to/root/samtools --prefix=/path/to/tophat --with-boost=/path/to/root/boost --with-boost-libdir=/path/to/boost/lib

(formatting comes out kinda funky on here. There should be no spaces except between flag options)

John
http://bioinformatics.plantbiology.msu.edu

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updated by Ram Ram • written by johnj • johnj

Thanks a lot for your help.

But after this I am getting another problem.. Its not finding bamlib though I gave the correct path to samtools using --with-bam option,. its giving error like this:-

configure: error: We could not detect the bam libraries (version or higher). If you have a staged bam library (still not installed) please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option.
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updated by Ram Ram • written by skdutta2091 • skdutta2091

Again, why don't you just download the precompiled binary?

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Sorry to say precompiled libraries are not getting downloaded as it is giving the following error:

The following NEW packages will be installed:
  libboost-thread1.54.0 tophat
0 upgraded, 2 newly installed, 0 to remove and 83 not upgraded.
Need to get 640 kB of archives.
After this operation, 3,821 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
WARNING: The following packages cannot be authenticated!
  libboost-thread1.54.0 tophat
Install these packages without verification? [y/N] y
Err http://archive.ubuntu.com/ubuntu/ trusty-updates/main libboost-thread1.54.0 amd64 1.54.0-4ubuntu3.1
  Cannot initiate the connection to archive.ubuntu.com:80 (2001:67c:1360:8c01::18). - connect (101: Network is unreachable) [IP: 2001:67c:1360:8c01::18 80]
Err http://archive.ubuntu.com/ubuntu/ trusty/universe tophat amd64 2.0.9-1ubuntu1
  Cannot initiate the connection to archive.ubuntu.com:80 (2001:67c:1360:8c01::18). - connect (101: Network is unreachable) [IP: 2001:67c:1360:8c01::18 80]
E: Failed to fetch http://archive.ubuntu.com/ubuntu/pool/main/b/boost1.54/libboost-thread1.54.0_1.54.0-4ubuntu3.1_amd64.deb  Cannot initiate the connection to archive.ubuntu.com:80 (2001:67c:1360:8c01::18). - connect (101: Network is unreachable) [IP: 2001:67c:1360:8c01::18 80]

E: Failed to fetch http://archive.ubuntu.com/ubuntu/pool/universe/t/tophat/tophat_2.0.9-1ubuntu1_amd64.deb  Cannot initiate the connection to archive.ubuntu.com:80 (2001:67c:1360:8c01::18). - connect (101: Network is unreachable) [IP: 2001:67c:1360:8c01::18 80]

E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
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updated by Ram Ram • written by skdutta2091 • skdutta2091

These (TopHat-2.1.0) binaries, provided by TopHat developers. Just unpack, add tophat to the PATH (or call it with its full path) and you are set.

Does the computer where you are trying to install has internet connection? It is failing to get the Ubuntu packages.

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updated by Ram Ram • written by h.mon h.mon

I would generally avoid using you system's package manager for bioinformatics software. You can typically get binaries from the web and they'll be more up to date.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

1 answer

Hello,

If you could answer these questions in as much detail as possible:

  • What is the system you are trying to install tophat on? i.e. linux? OSX? Windows?
  • What is the exact command you are using to attempt to install tophat?
  • What commands / methods did you use to install the Boost library?
  • Where did you install the Boost library?

Thanks,
Kyle

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updated by Ram Ram • written by mbio.kyle mbio.kyle

It's linux.

To install boost after unzipping the tar file I used the following commands:

./bootstrap.sh
./bjam --prefix=$HOME/local install

boost library is installed in the /home/local dir.

After unzipping the tarball file of tophat, I went to the folder of tophat using cd I used ./configure --with-boost=/home/local command. But it's not getting configured as it could not find boost library and giving that error which I mentioned earlier.

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updated by Ram Ram • written by skdutta2091 • skdutta2091

Unless there is some incompatibility, I would second Devon Ryan and strongly suggest you use the binaries.

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written by h.mon h.mon

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