Hi, David! I think that is right. There is no native support in BAM for HTTPS, but if it goes through our UCSC UDC layer with KNETFILE_HOOKS, it will get openssl support.
Search the email archives for information on compiling for BAM with KNETFILE_HOOKS. -Galt 11/23/2010 10:51 AM, David Hoover: > Do you think any of this has to do with KNETFILE_HOOKS? Do I need to > recompile samtools? > > David > > On Nov 23, 2010, at 12:39 PM, Galt Barber wrote: > >> >> Hi, David! >> >> 1. Do you have openssl installed? >> Is the make process correctly configured to compile and link it in? >> A quick check is to use ldd on one of your cgis such as hgTracks: >> >> ldd /usr/local/apache/cgi-bin/hgTracks >> libssl.so.6 => /lib64/libssl.so.6 >> libcrypto.so.6 => /lib64/libcrypto.so.6 >> libz.so.1 => /usr/lib64/libz.so.1 >> libm.so.6 => /lib64/libm.so.6 >> libc.so.6 => /lib64/libc.so.6 >> libgssapi_krb5.so.2 => /usr/lib64/libgssapi_krb5.so.2 >> libkrb5.so.3 => /usr/lib64/libkrb5.so.3 >> libcom_err.so.2 => /lib64/libcom_err.so.2 >> libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 >> libdl.so.2 => /lib64/libdl.so.2 >> /lib64/ld-linux-x86-64.so.2 >> libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 >> libkeyutils.so.1 => /lib64/libkeyutils.so.1 >> libresolv.so.2 => /lib64/libresolv.so.2 >> libselinux.so.1 => /lib64/libselinux.so.1 >> libsepol.so.1 => /lib64/libsepol.so.1 >> >> libssl, libcrypto, and several others in this list are related to openssl. >> >> Normally, if you try to access https with the kent libs >> and there is no openssl linked-in, it would generate >> an error message informing you of that. However, >> it's possible in this case that the error message >> got trapped and then replaced with a more generic >> error message. >> >> 2. Do you have a firewall that's blocking the https port? >> >> That is port 443 by default. >> >> -Galt >> >> 11/23/2010 8:39 AM, David Hoover: >>> Hi, >>> >>> I have a local mirror of the Genome Browser, and I can load an external BAM >>> file using the bigDataUrl directive: >>> >>> type=bam bigDataUrl=http://.../my.bam >>> >>> However, if I try to use https instead, >>> >>> type=bam bigDataUrl=https://.../my.bam >>> >>> it fails with the error message >>> >>> Error Can't access Ly2's bigDataUrl https://.../my.bam and/or the >>> associated index file https://.../my.bam.bai >>> >>> I know these files are accessible because I can download using wget from >>> the commandline of the web server machine that is running the local mirror. >>> >>> These commands work on the main UCSC Genome Browser, so what might be >>> different between the UCSC Genome Browser and our local mirror? >>> >>> Wondering, >>> David Hoover >>> Helix Systems Staff >>> http://helix.nih.gov >>> _______________________________________________ >>> Genome-mirror mailing list >>> [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
