Question: IOError: [Errno 93] could not open alignment file `https://...`: Protocol not supported
0
gravatar for jfreidin1
7 months ago by
jfreidin10
jfreidin10 wrote:

I have pysam code that works fine with pyenv-virtualenv on OSX but fails with miniconda2 on Centos:

IOError: [Errno 93] could not open alignment file `https://...`: Protocol not supported

After reading a lot of stuff I tried conda install libcurl (which worked), and then in pysam/, python setup.py install. It still complains:

Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.

I don't seem to be able to find a libcurl-devel package for conda and I don't have root access to install it. Any suggestions?

software error • 293 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by jfreidin10

Try fetching pysam with conda as well before digging deeper into this and see if it solves the issue.

ADD REPLYlink written 7 months ago by ATpoint21k

The first thing I tried:

conda install -y matplotlib pysam scikit-bio==0.4.2 pyensembl

That installed pysam==0.15.0 and worked fine for local bam files, but failed when I tried to open an https URL. I've attempted a few workarounds, including pip install -U pysam (0.15.1), uninstalling pysam from both conda and pip, and cloning the pysam repo and running python setup.py install (0.15.2). They all behave exactly the same way. If I could satisfy the libcurl-devel prerequisite I think I would be all set but I can't figure out how to do that without root access. I've also tried with and without HTSLIB_CONFIGURE_OPTIONS=--enable-plugins. I'm not entirely sure which one I should be using.

I'm running 0.15.2 built locally on OSX so I may need to build pysam locally anyway. It works on OSX because libcurl is present. Usually I can figure stuff like this out, but I'm completely stumped.

ADD REPLYlink modified 7 months ago • written 7 months ago by jfreidin10
0
gravatar for jfreidin1
7 months ago by
jfreidin10
jfreidin10 wrote:

Cloud Platform folks installed libcurl-devel for me. That worked.

ADD COMMENTlink written 7 months ago by jfreidin10
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