bcbio (1.2.9-2) unstable; urgency=medium * Team upload. * Fix watch file * Remove trailing whitespace in debian/changelog (routine-update) -- Andreas Tille Wed, 12 Oct 2022 09:38:21 +0200 bcbio (1.2.9-1) unstable; urgency=medium * Team Upload [ Lance Lin ] * New upstream version - 1.2.9 * Standards-Version: 4.6.1 * Copyright: updated years to cover 2022 -- Lance Lin Wed, 17 Aug 2022 20:16:42 +0700 bcbio (1.2.8-1) UNRELEASED; urgency=medium * New upstream version. * Standards-Version: 4.5.1 (routine-update) * Removed now obsolete patch on abc collections * Updated dependencies * Point to system version of Rscript - always -- Steffen Moeller Fri, 07 May 2021 20:29:57 +0200 bcbio (1.2.5-1) unstable; urgency=medium * New upstream version. -- Steffen Moeller Tue, 26 Jan 2021 13:55:23 +0100 bcbio (1.2.4-3) UNELEASED; urgency=medium * Compatibility with Python 3.9 * Rounded-up Debian experience - Added runtime/testing build depdendencies - Adjusted names of executables in Debian + hts-nim-tools + cnvkit -- Steffen Moeller Sat, 14 Nov 2020 22:29:00 +0100 bcbio (1.2.4-2) unstable; urgency=medium * Team upload. * Avoid calling Git - use Debian version to specify the code version Closes: #973804 -- Andreas Tille Fri, 06 Nov 2020 11:16:33 +0100 bcbio (1.2.4-1) unstable; urgency=medium * New upstream version * debhelper-compat 13 (routine-update) -- Steffen Moeller Sat, 26 Sep 2020 00:56:30 +0200 bcbio (1.2.0-2) unstable; urgency=medium * Team upload. * Drop tophat from Build-Depends Closes: #953642 * Add salsa-ci file (routine-update) -- Andreas Tille Wed, 11 Mar 2020 18:26:32 +0100 bcbio (1.2.0-1) unstable; urgency=medium * New upstream version * debhelper-compat 12 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Remove trailing whitespace in debian/copyright (routine-update) * Remove trailing whitespace in debian/rules (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Adjusted path of bcbio-doc for doc-base -- Steffen Moeller Thu, 13 Feb 2020 18:30:04 +0100 bcbio (1.1.9-2) unstable; urgency=medium * Team upload. * Drop tophat. -- Michael R. Crusoe Fri, 14 Feb 2020 17:23:23 +0100 bcbio (1.1.9-1) unstable; urgency=medium * New upstream version. * Updated d/watch -- Steffen Moeller Wed, 11 Dec 2019 11:39:46 +0100 bcbio (1.1.8-1) unstable; urgency=medium * New upstream version. -- Steffen Moeller Tue, 26 Nov 2019 14:05:42 +0100 bcbio (1.1.7-1) unstable; urgency=medium * New upstream version. * Added directions to contrib to -doc and python- packages -- Steffen Moeller Sat, 19 Oct 2019 14:02:34 +0200 bcbio (1.1.5-1) unstable; urgency=medium * New upstream version. * Better clean after build * Tests still fail. -- Steffen Moeller Fri, 24 May 2019 18:42:30 +0200 bcbio (1.1.4-2) UNRELEASED; urgency=medium * Team upload. * Recommends: umis -- Andreas Tille Thu, 16 May 2019 09:49:26 +0200 bcbio (1.1.4-1) unstable; urgency=medium * New upstream release. - Move to Python 3.6. A python2 environment in the install runs non python3 compatible programs. The codebase is still compatible with python 2.7 but will only get run and tested on python 3 for future releases. - RNA-seq: fix for race condition when creating the pizzly cache - RNA-seq: Add Salmon to multiqc report. - RNA-seq single-cell/DGE: Properly strip transcript versions from GENCODE GTFs. - RNA-seq: Faster and more flexible rRNA biotype lookup. - Move to R3.5.1, including updates to all CRAN and Bioconductor packages. - tumor-only germline prioritization: provide more useful germline filtering based on prioritization INFO tag (EPR) rather than filter field. - Install: do not require fabric for tool and data installs, making full codebase compatible with python 3. - variant: Filter out variants with missing ALT alleles output by GATK4. - GATK: enable specification of spark specific parameters with `gatk-spark` resources. - RNA-seq single-cell/DGE: added `demultiplexed` option. If set to True, treat the data as if it has already been demultiplexed into cells/wells. - Multiple orders of magnitude faster templating with thousands of input files. * Moved stringtie from suggested to recommended * Added dependency on xonsh for testing -- Steffen Moeller Thu, 11 Apr 2019 12:56:58 +0200 bcbio (1.1.3-1) unstable; urgency=medium * Team upload. * New upstream release. * bcbio-doc: mark as "Multi-Arch: foreign" * debian/patches/python3.patch: removed, applied upstream * debian/control: bcbio-doc: section is "doc" and add ${sphinxdoc:Built-Using} python3-bcbio: section is "python" * debian/patches/spelling: fix a few spelling errors * debian/patches/include_tests -- Michael R. Crusoe Sun, 10 Feb 2019 00:42:06 -0800 bcbio (1.1.2-3) unstable; urgency=medium * Demoted python3-seqcluster to become a recommendation * Packaged documentation, which also contributed a man page -- Steffen Moeller Wed, 23 Jan 2019 15:04:57 +0100 bcbio (1.1.2-2) UNRELEASED; urgency=medium * Found Python3 incompatbility. Upstream has it already. -- Steffen Moeller Mon, 21 Jan 2019 23:56:26 +0100 bcbio (1.1.2-1) UNRELEASED; urgency=medium * Initial release (Closes: #903386) TODO: Documentation not built -- Steffen Moeller Thu, 17 Jan 2019 16:37:37 +0100