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isdb's Introduction

ISDB is an open-source software toolkit for building databases of proviral integration sites.

Using ISDB, you can curate a private database from any heterogenous set of data sources, including previously-published datasets and internal, work-in-progress data. To make data visible and accessible to collaborators with varying degrees of computational expertise, ISDB automatically generates web sites describing database contents and data exports in several common formats.

As distinct from a public depository database, the ability to build local, private databases makes ISDB suitable for use in testing hypotheses and developing analyses in the long pre-publication phase of most research. The goal of ISDB is to provide a standard end-to-end platform for reliably storing, performing reproducible analyses on, and ultimately publishing integration site data.

We developed ISDB to support our research into the locations of HIV-1 proviral integrations in patients on suppressive ART. It helps us durably store and reliably manage the data we generate and provides a standard platform for our analyses across datasets.

HIRIS, our HIV-1 Reservoirs Integration Sites database, is built and published using ISDB.

Please see the ISDB website for more information, including how to get started and other documentation.

isdb's People

Contributors

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Stargazers

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Watchers

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Forkers

tsibley roryk wangdi2014 tongyt1225

isdb's Issues

Website should be fully-functional when served from the filesystem

Currently it's mostly functional when served over the filesystem instead of over HTTP, but there's no good reason it can't be fully functional. This would make previewing the website much simpler, especially for non-developers or developers unfamiliar with webservers.

website generation not working, OSX high sierra system perl

Heya, the website generation doesn't work for me under using OSX high sierra with the system perl.

./bin/generate-website output-directory
Output to: output-directory
Writing version metadata: latest
Exporting data
Exporting: Summary by gene…
Exporting: Integration summary…
Exporting: Integration summary with annotated genes…
Exporting BED for Genome Browser
Module::Pluggable::Object will be removed from the Perl core distribution in the next major release. Please install it from CPAN. It is being used at /System/Library/Perl/Extras/5.18/Config/Any.pm, line 7.
Module::Pluggable::Object will be removed from the Perl core distribution in the next major release. Please install it from CPAN. It is being used at /System/Library/Perl/Extras/5.18/Config/Any.pm, line 7.
Exporting GFF for each gene
5693 files written
Zipping up GFF per gene
Caching stats
Caching table metadata
Caching PubMed info
Can't load '/Users/rory/cache/ISDB/bin/../local/lib/perl5/darwin-thread-multi-2level/auto/Net/Curl/Curl.bundle' for module Net::Curl: dlopen(/Users/rory/cache/ISDB/bin/../local/lib/perl5/darwin-thread-multi-2level/auto/Net/Curl/Curl.bundle, 1): Library not loaded: @rpath/libcurl.4.dylib
  Referenced from: /Users/rory/cache/ISDB/local/lib/perl5/darwin-thread-multi-2level/auto/Net/Curl/Curl.bundle
  Reason: image not found at /System/Library/Perl/5.18/darwin-thread-multi-2level/DynaLoader.pm line 194.
 at /Users/rory/cache/ISDB/bin/../local/lib/perl5/darwin-thread-multi-2level/Net/Curl.pm line 33.
BEGIN failed--compilation aborted at /Users/rory/cache/ISDB/bin/../local/lib/perl5/darwin-thread-multi-2level/Net/Curl.pm line 33.
Compilation failed in require at /Users/rory/cache/ISDB/bin/../local/lib/perl5/darwin-thread-multi-2level/Net/Curl/Easy.pm line 5.
BEGIN failed--compilation aborted at /Users/rory/cache/ISDB/bin/../local/lib/perl5/darwin-thread-multi-2level/Net/Curl/Easy.pm line 5.
Compilation failed in require at /Users/rory/cache/ISDB/bin/../local/lib/perl5/LWP/Protocol/Net/Curl.pm line 16.
BEGIN failed--compilation aborted at /Users/rory/cache/ISDB/bin/../local/lib/perl5/LWP/Protocol/Net/Curl.pm line 16.
Compilation failed in require at /Users/rory/cache/ISDB/bin/cache-pubmed-info line 11.
BEGIN failed--compilation aborted at /Users/rory/cache/ISDB/bin/cache-pubmed-info line 11.

I also couldn't get it working with the Postgres.app and had to load it via homebrew:

brew install postgres
brew services start postgresql

any tips getting this working?

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