Accessing ENCODE files on Mac; issue with curl? about pybigwig

[lavenderca]

Currently trying an upgrade.

[dpryan79]

Interesting, this is likely unrelated to the redirect but instead related to a certificate error in OSX. Did you install pyBigWig with bioconda or pip?

[lavenderca]

bioconda. I used the following:
conda install pybigwig -c bioconda

[dpryan79]

What's the output of conda list | grep curl?

[lavenderca]

$ conda list | grep curl
curl                      7.45.0                        0  
pycurl                    7.19.5.3                 py34_0  

[dpryan79]

What happens if you conda install -c bioconda curl (you might have to remove the one you currently have installed)? I made a version of curl for bioconda a year or so ago that fixed a few problems like this.

[lavenderca]

The upgrade seems to work! Thanks so much for your help.

Ran conda upgrade curl. Now:

$ conda list | grep curl
curl                      7.52.1                        0  
pycurl                    7.43.0                   py34_2

[dpryan79]

Cool, conda finally fixed their package! Glad that worked!

[kepbod]

Hi! I came up with the same question even after I upgraded curl. How shall I solve this problem? Many thanks!

$ conda list | grep curl
curl                      7.52.1                        0    defaults
pycurl                    7.43.0                   py35_2    defaults

[dpryan79]

What version of OSX are both of you using? Maybe that's the difference? Perhaps I should add an option to libBigWig (what pyBigWig uses) to ignore certificate errors.

[kepbod]

I download some bigwig files from ENCODE, and some of them works, but some are not. In addition, using url directly works well.
For example:

pyBigWig.open('https://www.encodeproject.org/files/ENCFF555VCB/@@download/ENCFF555VCB.bigWig')

works well.

pyBigWig.open('ENCFF555VCB.bigwig')

could not work after I download the file to my server.
The error message is:

[urlOpen] Couldn't open ENCFF555VCB.bigwig for reading

Sorry, this problem occurs in linux server.

[dpryan79]

Are you in the same directory as ENCFF555VCB.bigwig?

[kepbod]

Yes. In addition, I am wondering whether it is because the version of my installed pybigwig is too low. I installed it via bioconda, and the latest version of pybigwig is 0.2.8 in bioconda.

[dpryan79]

@kepbod: You'll get that error whenever there's an error opening a local file. This particular error will usually only happen if the file specified doesn't exist or you don't have rights to open it.

[kepbod]

Oh, it is my fault. I figured out what is wrong that I used the wrong file name. Thanks for your assistance.