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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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Ubuntu 18.04 Can't install this JBrowser-1.16.10 #1551

Closed linjiahao962889027 closed 3 years ago

linjiahao962889027 commented 3 years ago

My Quesetion

Gathering system information ...done. NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier. Minimal release, skipping node and Webpack build (note: this version will not allow using plugins. Use a github clone or a dev version of JBrowse to use plugins Installing Perl prerequisites ... failed. See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

Formatting Volvox example data ... failed. See setup.log file for error messages.

Formatting Yeast example data ... failed. See setup.log file for error messages.

Issue

I try my best to install JBrowser，but I failed. operating system： No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.5 LTS Release: 18.04 Codename: bionic WSL2，Windows10（2004，19041.508）

setup.log

Gathering system information ... ============== System information ====

done.

NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.

Minimal release, skipping node and Webpack build (note: this version will not allow using plugins. Use a github clone or a dev version of JBrowse to use plugins

Installing Perl prerequisites ...

Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Searching Bio::Perl (== 1.7.2) on cpanmetadb ... --2020-10-12 23:56:57-- http://cpanmetadb.plackperl.org/v1.0/history/Bio::Perl Resolving cpanmetadb.plackperl.org (cpanmetadb.plackperl.org)... 151.101.110.217 Connecting to cpanmetadb.plackperl.org (cpanmetadb.plackperl.org)|151.101.110.217|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 792 [text/plain] Saving to: ‘STDOUT’

 0K                                                       100% 46.1M=0s

2020-10-12 23:56:57 (46.1 MB/s) - written to stdout [792/792]

--> Working on Bio::Perl Fetching http://backpan.perl.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz ... --2020-10-12 23:56:57-- http://backpan.perl.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz Resolving backpan.perl.org (backpan.perl.org)... failed: Temporary failure in name resolution. wget: unable to resolve host address ‘backpan.perl.org’ Unpacking BioPerl-1.007002.tar.gz OK

gzip: stdin: unexpected end of file /bin/tar: Child returned status 1 /bin/tar: Error is not recoverable: exiting now ! Failed to unpack BioPerl-1.007002.tar.gz: no directory Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz ... --2020-10-12 23:57:07-- http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz Resolving www.cpan.org (www.cpan.org)... failed: Temporary failure in name resolution. wget: unable to resolve host address ‘www.cpan.org’ Unpacking BioPerl-1.007002.tar.gz OK

gzip: stdin: unexpected end of file /bin/tar: Child returned status 1 /bin/tar: Error is not recoverable: exiting now ! Failed to unpack BioPerl-1.007002.tar.gz: no directory ! Failed to fetch distribution BioPerl-1.007002

Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Searching Bio::Perl (== 1.7.2) on cpanmetadb ... --2020-10-12 23:57:17-- http://cpanmetadb.plackperl.org/v1.0/history/Bio::Perl Resolving cpanmetadb.plackperl.org (cpanmetadb.plackperl.org)... failed: Temporary failure in name resolution. wget: unable to resolve host address ‘cpanmetadb.plackperl.org’ Searching Bio::Perl (== 1.7.2) on metacpan ... --2020-10-12 23:57:27-- http://api.metacpan.org/v0/file/_search?source=%7B%22query%22%3A%7B%22filtered%22%3A%7B%22query%22%3A%7B%22nested%22%3A%7B%22query%22%3A%7B%22custom_score%22%3A%7B%22query%22%3A%7B%22constant_score%22%3A%7B%22filter%22%3A%7B%22and%22%3A%5B%7B%22term%22%3A%7B%22module.authorized%22%3Atrue%7D%7D%2C%7B%22term%22%3A%7B%22module.indexed%22%3Atrue%7D%7D%2C%7B%22term%22%3A%7B%22module.name%22%3A%22Bio%3A%3APerl%22%7D%7D%2C%7B%22term%22%3A%7B%22module.version%22%3A%22v1.7.2%22%7D%7D%5D%7D%7D%7D%2C%22metacpan_script%22%3A%22score_version_numified%22%7D%7D%2C%22score_mode%22%3A%22max%22%2C%22path%22%3A%22module%22%7D%7D%7D%7D%2C%22fields%22%3A%5B%22date%22%2C%22release%22%2C%22author%22%2C%22module%22%2C%22status%22%5D%7D Resolving api.metacpan.org (api.metacpan.org)... failed: Temporary failure in name resolution. wget: unable to resolve host address ‘api.metacpan.org’ ! Could not find a release matching Bio::Perl (== 1.7.2) on MetaCPAN. Searching Bio::Perl on mirror http://www.cpan.org ... Downloading index file http://www.cpan.org/modules/02packages.details.txt.gz ... --2020-10-12 23:57:37-- http://www.cpan.org/modules/02packages.details.txt.gz Resolving www.cpan.org (www.cpan.org)... 151.101.110.217, 2a04:4e42:36::729 Connecting to www.cpan.org (www.cpan.org)|151.101.110.217|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 2341147 (2.2M) [application/x-gzip] Saving to: ‘/home/linjiahao/.cpanm/sources/http%www.cpan.org/02packages.details.txt.gz’

 0K .......... .......... .......... .......... ..........  2%  197K 11s
50K .......... .......... .......... .......... ..........  4%  376K 8s

100K .......... .......... .......... .......... .......... 6% 217K 9s 150K .......... .......... .......... .......... .......... 8% 641K 7s 200K .......... .......... .......... .......... .......... 10% 208K 8s 250K .......... .......... .......... .......... .......... 13% 469K 7s 300K .......... .......... .......... .......... .......... 15% 139K 8s 350K .......... .......... .......... .......... .......... 17% 120K 9s 400K .......... .......... .......... .......... .......... 19% 90.8K 10s 450K .......... .......... .......... .......... .......... 21% 128K 10s 500K .......... .......... .......... .......... .......... 24% 74.6K 11s 550K .......... .......... .......... .......... .......... 26% 100K 11s 600K .......... .......... .......... .......... .......... 28% 121K 11s 650K .......... .......... .......... .......... .......... 30% 121K 11s 700K .......... .......... .......... .......... .......... 32% 172K 10s 750K .......... .......... .......... .......... .......... 34% 144K 10s 800K .......... .......... .......... .......... .......... 37% 180K 10s 850K .......... .......... .......... .......... .......... 39% 185K 9s 900K .......... .......... .......... .......... .......... 41% 169K 9s 950K .......... .......... .......... .......... .......... 43% 142K 8s 1000K .......... .......... .......... .......... .......... 45% 122K 8s 1050K .......... .......... .......... .......... .......... 48% 182K 8s 1100K .......... .......... .......... .......... .......... 50% 153K 8s 1150K .......... .......... .......... .......... .......... 52% 164K 7s 1200K .......... .......... .......... .......... .......... 54% 146K 7s 1250K .......... .......... .......... .......... .......... 56% 123K 7s 1300K .......... .......... .......... .......... .......... 59% 178K 6s 1350K .......... .......... .......... .......... .......... 61% 212K 6s 1400K .......... .......... .......... .......... .......... 63% 146K 5s 1450K .......... .......... .......... .......... .......... 65% 162K 5s 1500K .......... .......... .......... .......... .......... 67% 135K 5s 1550K .......... .......... .......... .......... .......... 69% 105K 5s 1600K .......... .......... .......... .......... .......... 72% 114K 4s 1650K .......... .......... .......... .......... .......... 74% 138K 4s 1700K .......... .......... .......... .......... .......... 76% 158K 4s 1750K .......... .......... .......... .......... .......... 78% 104K 3s 1800K .......... .......... .......... .......... .......... 80% 148K 3s 1850K .......... .......... .......... .......... .......... 83% 89.6K 3s 1900K .......... .......... .......... .......... .......... 85% 109K 2s 1950K .......... .......... .......... .......... .......... 87% 131K 2s 2000K .......... .......... .......... .......... .......... 89% 147K 2s 2050K .......... .......... .......... .......... .......... 91% 116K 1s 2100K .......... .......... .......... .......... .......... 94% 142K 1s 2150K .......... .......... .......... .......... .......... 96% 145K 1s 2200K .......... .......... .......... .......... .......... 98% 171K 0s 2250K .......... .......... .......... ...... 100% 157K=16s

2020-10-12 23:57:57 (143 KB/s) - ‘/home/linjiahao/.cpanm/sources/http%www.cpan.org/02packages.details.txt.gz’ saved [2341147/2341147]

Uncompressing index file... Found Bio::Perl 1.007004 which doesn't satisfy == 1.7.2.

Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Searching Bio::Perl (== 1.7.2) on cpanmetadb ... --2020-10-12 23:57:58-- http://cpanmetadb.plackperl.org/v1.0/history/Bio::Perl Resolving cpanmetadb.plackperl.org (cpanmetadb.plackperl.org)... 151.101.78.217 Connecting to cpanmetadb.plackperl.org (cpanmetadb.plackperl.org)|151.101.78.217|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 792 [text/plain] Saving to: ‘STDOUT’

 0K                                                       100% 54.0M=0s

2020-10-12 23:57:58 (54.0 MB/s) - written to stdout [792/792]

--> Working on Bio::Perl Fetching http://backpan.perl.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz ... --2020-10-12 23:57:58-- http://backpan.perl.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz Resolving backpan.perl.org (backpan.perl.org)... failed: Temporary failure in name resolution. wget: unable to resolve host address ‘backpan.perl.org’ Unpacking BioPerl-1.007002.tar.gz OK

gzip: stdin: unexpected end of file /bin/tar: Child returned status 1 /bin/tar: Error is not recoverable: exiting now ! Failed to unpack BioPerl-1.007002.tar.gz: no directory Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz ... --2020-10-12 23:58:08-- http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz Resolving www.cpan.org (www.cpan.org)... failed: Temporary failure in name resolution. wget: unable to resolve host address ‘www.cpan.org’ Unpacking BioPerl-1.007002.tar.gz OK

gzip: stdin: unexpected end of file /bin/tar: Child returned status 1 /bin/tar: Error is not recoverable: exiting now ! Failed to unpack BioPerl-1.007002.tar.gz: no directory ! Failed to fetch distribution BioPerl-1.007002

Formatting Volvox example data ...

Formatting Yeast example data ...

Quickly

I hope I can get help quickly.

cmdcolin commented 3 years ago

@linjiahao962889027 Hi there

There seem to be several domain resolution errors

"Resolving backpan.perl.org (backpan.perl.org)... failed: Temporary failure in name resolution." "Resolving api.metacpan.org (api.metacpan.org)... failed: Temporary failure in name resolution." "Resolving www.cpan.org (www.cpan.org)... failed: Temporary failure in name resolution."

You could re-try running setup.sh and see if these go away?

Alternatively, note that you do not need the Perl tools of jbrowse. You can use jbrowse without running prepare-refseqs.pl or flatfile-to-json.pl, etc. Using generate-names.pl is helpful though.

For general track purposes, you can use indexed file formats such as indexed BAM, tabix VCF, indexed FASTA, bigwig, tabix GFF3 etc. and these do not require perl loading scripts, just hand editing the config file. Your jbrowse is likely already setup, just without the sample data.

See this tutorial for the indexed file formats tutorial https://jbrowse.org/docs/tutorial.html

See this for the "classic quick start guide" which uses the perl loading scripts https://jbrowse.org/docs/tutorial_classic.html

linjiahao962889027 commented 3 years ago

@cmdcolin You are right, according to your tutorial, I loading indexed fasta. Maybe , I can't visit the backpan.perl.org and api.metacpan.org by using Chinese net. But the information from the setup.sh is very unfriendly，I still consider it maybe cause by defected the dependency package/lib. And I install all the libraries that the Jbrowse needed. In fact I try use those command:

rm -rf extlib
bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
./setup.sh

and

rm -rf extlib # inside the jbrowse directory
cpanm https://github.com/bioperl/bioperl-live/archive/release-1-7-2.tar.gz
./setup.sh

to resolving my problem. When I use cpanm https://github.com/bioperl/bioperl-live/archive/release-1-7-2.tar.gz, the system remind me that I success，but the setup.sh still give me the same information which remind me that I failed. I think it might be better to integrate Perl program dependency packages that need to be installed over the network into the installation package.

cmdcolin commented 3 years ago

The BioPerl installation is pinned to 1.7.2 which is kind of annoying and should probably be made a bit better. We have to manually use BioPerl@1.7.2 because BioPerl@1.7.3 and later drastically reorganized the BioPerl installation (see https://metacpan.org/changes/distribution/BioPerl)

If we upgraded to the latest BioPerl it might help things somewhat, I can't recall what is holding us back