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rwdavies / STITCH

STITCH - Sequencing To Imputation Through Constructing Haplotypes
http://www.nature.com/ng/journal/v48/n8/abs/ng.3594.html
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STITCH 1.6.3 conda install seems to need libiconv for rsync to work #38

Closed jelber2 closed 3 years ago

jelber2 commented 3 years ago

Hi,

I originally installed STITCH 1.6.3 with the following conda command

conda create -n STITCH1.6.3 r-stitch=1.6.3 -c defaults -c bioconda -c conda-forge

but STITCH complained that rsync couldn't access library libiconv.so.2.

thus the following would have worked in my case on a Ubuntu 16.04.7 system

conda create -n STITCH1.6.3 r-stitch=1.6.3 libiconv -c defaults -c bioconda -c conda-forge

Not sure if others have had this problem or not?

rwdavies commented 3 years ago

Huh, this is weird. This feels like an rsync package problem? Am I right that Ubuntu 16.04.7 is very new?

What about if you try just installing conda rsync in a clean environment, does that work?

jelber2 commented 3 years ago

Yes, Ubuntu 16.04.7 is very new. I made a clean environment just installing rsync and dependencies and it worked fine. Weird.

rwdavies commented 3 years ago

huh, this is so weird, rsync conda doesn't seem to have changed in a year. and libiconv seems to install the same thing from rsync and r-stitch? I just tried this on a linux box (older), with just doing conda rsync or conda r-stitch, and they both seem to have an libiconv

conda rsync

(base) rdavies@smew:~$ldd /data/smew1/rdavies/miniconda3/bin/rsync
...
        libiconv.so.2 => /data/smew1/rdavies/miniconda3/bin/../lib/libiconv.so.2 (0x00007f7970f6b000)

conda r-stitch

(test_stitch_only) rdavies@smew:~$which rsync
/data/smew1/rdavies/miniconda3/envs/test_stitch_only/bin/rsync
(test_stitch_only) rdavies@smew:~$ldd /data/smew1/rdavies/miniconda3/envs/test_stitch_only/bin/rsync
...
        libiconv.so.2 => /data/smew1/rdavies/miniconda3/envs/test_stitch_only/bin/../lib/libiconv.so.2 (0x00007fe80e253000)

also they have the same md5

I've got STITCH 1.6.5 going through bioconda now so hopefully that no longer has this issue?

jelber2 commented 3 years ago

I don't really know what the problem was- maybe something to do with Ubuntu, I don't know?