libboost 1.57

[lfaller]

Hi all,

I got the following error message when running sailfish:

/home/qiime/local/bin/sailfish index -p 1 -t /home/qiime/bioinfohd1/freire_lab/neutrophil_project/small_example/input/h_vs_td2_small-merged/work/sailfish/16_D/index/GRCh37/GRCh37.fa -o /home/qiime/bioinfohd1/freire_lab/neutrophil_project/small_example/input/h_vs_td2_small-merged/work/sailfish/16_D/index/tx/tmp8z4XtN/GRCh37 -k 25

/home/qiime/local/bin/sailfish: error while loading shared libraries: libboost_iostreams.so.1.57.0: cannot open shared object file: No such file or directory
' returned non-zero exit status 127

I have the following versions of libboost installed:

$> locate libboost_iostreams
/home/lfaller/local/share/bcbio/anaconda/lib/libboost_iostreams.so
/home/lfaller/local/share/bcbio/anaconda/lib/libboost_iostreams.so.1.60.0
/home/lfaller/local/share/bcbio/anaconda/pkgs/boost-1.60.0-py27_0/lib/libboost_iostreams.so
/home/lfaller/local/share/bcbio/anaconda/pkgs/boost-1.60.0-py27_0/lib/libboost_iostreams.so.1.60.0
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.54.0

I believe 1.60 is the most recent version. Does sailfish not support that?
I am running Ubuntu 14.04.3 LTS (trusty) and I'm not seeing 1.57 in the list of available packages (http://packages.ubuntu.com/search?suite=trusty&arch=any&searchon=names&keywords=libboost-system).

Any suggestion you might have is much appreciated!

Best,
~Lina

[rob-p]

Hi Lina,

Sailfish should be compatible with the most recent version of Boost (it just requires a version >= 1.54). However, the problem here seems to be that it was built against 1.57, which it's looking for explicitly, and it's only able to find 1.60. Could you tell me what version of Sailfish you're using, and if it was compiled from source or installed as a pre-compiled binary? I ask because we've been building the pre-compiled binaries with static linking for a while now to avoid just this type of issue.

Best,
Rob

[lfaller]

Hi Rob,

Thanks for your quick reply!

I installed sailfish as part of bcbio-nextgen (https://github.com/chapmanb/bcbio-nextgen) so I'm not sure how the install actually worked (maybe @roryk or @lpantano might know?)

Checking for the version doesn't seem to work on my system at this stage:

/home/qiime/local/bin/sailfish --version
/home/qiime/local/bin/sailfish: error while loading shared libraries: libboost_iostreams.so.1.57.0: cannot open shared object file: No such file or directory

Would you recommend that reinstalling one of the compiled binaries is the way to go?

Thanks a bunch!

[lpantano]

Hi @lfaller,

I think you need to ping https://github.com/bioconda/bioconda-recipes. Maybe is an easy problem of just updating the build or the package.

I guess this happened after an update? If not, I would try to update everything again.

I will try to investigate as well!

[roryk]

In the bioconda formula we tried to remove downloading boost and dynamically link to the bioconda boost, but I guess it ended up linking to a specific version of boost. I tried to swap it to statically linked to the bioconda boost, but no combination of -DBOOST_INCLUDEDIR and -DBOOST_LIBDIR would find boost. I'm testing just statically linking it now to the Sailfish/Salmon downloaded boost.

[lfaller]

Thanks for all the help!

@lpantano, I ran the update command and got the following:

./bcbio_conda update bcbio-nextgen
Fetching package metadata: ....
# All requested packages already installed.
# packages in environment at /home/lfaller/local/share/bcbio/anaconda:
#
bcbio-nextgen             0.9.6                    py27_0    bioconda

So it looks like I'm already using the most recent version.

[lpantano]

As @roryk discovered, you can install the previous version: path_to_bcbio_anaconda_bin/conda install boost=1.57.0 -c bioconda and should work this way. I think we were implementing that in the installation but this should get you ready to work again.

[lfaller]

Thanks @lpantano, I think this did the trick! Much appreciated!