Comments (4)
dancooke
commented on August 30, 2024
1
I'm closing this issue as the problem is not with octopus and I do not maintain the Bioconda recipe. I suggest opening an issue on the Bioconda Github page if the problem persists.
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dancooke
commented on August 30, 2024
Which operating system are you using? I can try to look into this, but I don't maintain the Bioconda package. @chapmanb might be able to help?
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micknudsen
commented on August 30, 2024
My example was run on Centos Linux:
[michaelk@fe1 ~]$ cat /proc/version
Linux version 2.6.32-642.1.1.el6.x86_64 ([email protected]) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC) ) #1 SMP Tue May 31 21:57:07 UTC 2016
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chapmanb
commented on August 30, 2024
Michael;
Sorry about the issue, this is built on CentOS6 so should be compatible. The tricky bit is that octopus compiles against gcc 7 which get installed within the conda environment and then it should link against those. This all should happen cleanly but seems not to in your case.
A couple of thoughts:
- Could you try running directly instead of using
source activate? I've found a lot of issues with trying to use environments if you end up having other environmental variables set or multiple environments, so that could help isolate if there is some kind of cross-environment interference going on. - You could also take a look and be sure the libraries resolve to the correct place:
ldd /home/michaelk/anaconda3/envs/octopus/bin/octopus. This might reveal something cross-wired. For comparison, here's what mine looks like
$ ldd /usr/local/share/bcbio/anaconda/bin/octopus
linux-vdso.so.1 => (0x00007ffc6e9d9000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f32e0cfa000)
libboost_system.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/libboost_system.so.1.65.0 (0x00007f32e0af5000)
libboost_filesystem.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/libboost_filesystem.so.1.65.0 (0x00007f32e08d9000)
libboost_program_options.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/libboost_program_options.so.1.65.0 (0x00007f32e065f000)
libboost_log_setup.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/libboost_log_setup.so.1.65.0 (0x00007f32e03b8000)
libboost_log.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/libboost_log.so.1.65.0 (0x00007f32e00d9000)
libboost_timer.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/libboost_timer.so.1.65.0 (0x00007f32dfed3000)
libboost_thread.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/libboost_thread.so.1.65.0 (0x00007f32dfcb0000)
libhts.so.2 => /usr/local/share/bcbio/anaconda/bin/../lib/libhts.so.2 (0x00007f32df9e3000)
libstdc++.so.6 => /usr/local/share/bcbio/anaconda/bin/../lib/libstdc++.so.6 (0x00007f32df6a9000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f32df3a0000)
libgcc_s.so.1 => /usr/local/share/bcbio/anaconda/bin/../lib/libgcc_s.so.1 (0x00007f32df18e000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f32def71000)
/lib64/ld-linux-x86-64.so.2 (0x00007f32e17d3000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f32ded69000)
libboost_regex.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/./libboost_regex.so.1.65.0 (0x00007f32dea67000)
libboost_date_time.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/./libboost_date_time.so.1.65.0 (0x00007f32de854000)
libboost_chrono.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/./libboost_chrono.so.1.65.0 (0x00007f32de64f000)
libboost_atomic.so.1.65.0 => /usr/local/share/bcbio/anaconda/bin/../lib/./libboost_atomic.so.1.65.0 (0x00007f32de44d000)
libicudata.so.58 => /usr/local/share/bcbio/anaconda/bin/../lib/./libicudata.so.58 (0x00007f32dc94d000)
libicui18n.so.58 => /usr/local/share/bcbio/anaconda/bin/../lib/./libicui18n.so.58 (0x00007f32dc44d000)
libicuuc.so.58 => /usr/local/share/bcbio/anaconda/bin/../lib/./libicuuc.so.58 (0x00007f32dc04e000)
liblzma.so.5 => /usr/local/share/bcbio/anaconda/bin/../lib/./liblzma.so.5 (0x00007f32dbe2a000)
libbz2.so.1.0 => /usr/local/share/bcbio/anaconda/bin/../lib/./libbz2.so.1.0 (0x00007f32dbc1a000)
libz.so.1 => /usr/local/share/bcbio/anaconda/bin/../lib/./libz.so.1 (0x00007f32db9fd000)
libcurl.so.4 => /usr/local/share/bcbio/anaconda/bin/../lib/./libcurl.so.4 (0x00007f32db78a000)
libcrypto.so.1.0.0 => /usr/local/share/bcbio/anaconda/bin/../lib/./libcrypto.so.1.0.0 (0x00007f32db33a000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f32db136000)
libssh2.so.1 => /usr/local/share/bcbio/anaconda/bin/../lib/././libssh2.so.1 (0x00007f32daefd000)
libssl.so.1.0.0 => /usr/local/share/bcbio/anaconda/bin/../lib/././libssl.so.1.0.0 (0x00007f32dac84000)
libgssapi_krb5.so.2 => /usr/local/share/bcbio/anaconda/bin/../lib/././libgssapi_krb5.so.2 (0x00007f32daa3c000)
libkrb5.so.3 => /usr/local/share/bcbio/anaconda/bin/../lib/././libkrb5.so.3 (0x00007f32da771000)
libk5crypto.so.3 => /usr/local/share/bcbio/anaconda/bin/../lib/././libk5crypto.so.3 (0x00007f32da543000)
libcom_err.so.3 => /usr/local/share/bcbio/anaconda/bin/../lib/././libcom_err.so.3 (0x00007f32da340000)
libkrb5support.so.0 => /usr/local/share/bcbio/anaconda/bin/../lib/./././libkrb5support.so.0 (0x00007f32da135000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f32d9f1a000)
Hope this helps.
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