[med-svn] [Git][med-team/qiime][master] Delete old Qiime dependencies

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / qiime


Commits:
1ae71cf2 by Liubov Chuprikova at 2019-03-11T22:16:02Z
Delete old Qiime dependencies

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+qiime (2019.1.0-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Delete old Qiime dependencies
+
+ -- Liubov Chuprikova <chuprikovalv at gmail.com>  Tue, 12 Mar 2019 00:13:16 +0200
+
 qiime (2019.1.0-1) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/control
=====================================
@@ -27,77 +27,30 @@ Depends: ${shlibs:Depends},
          ${python3:Depends},
          python3-bibtexparser,
          python3-decorator,
-         python3-matplotlib,
-         python3-numpy,
          python3-pandas,
          python3-tzlocal,
          python3-yaml,
-         python-burrito,
-         python-burrito-fillings (>= 0.1.1),
-         python-biom-format,
-         python-cogent (>= 1.5.3),
-         python-mpi4py,
-         python-qcli,
-         pynast (>= 1.2.2),
-         qiime-data,
-         ampliconnoise,
-         blast2 | blast+-legacy,
-         bwa,
-         cd-hit,
-         chimeraslayer,
-         clearcut,
-         clustalw,
-         ea-utils,
-         emperor (>= 0.9.51),
-         fasttree,
-         infernal,
-         libjs-jquery,
-         mafft,
-         muscle,
-         parsinsert,
-         raxml,
-         r-cran-optparse,
-         rdp-classifier,
-         seqprep,
-         sortmerna,
-         sumatra,
-         swarm,
-         vsearch
-Recommends: mothur,
-            rtax
-Suggests: t-coffee,
-          cytoscape,
-          torque-client,
-          qiime-default-reference
+         python3-pyparsing,
+         python3-dateutil
 Description: Quantitative Insights Into Microbial Ecology
- QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
- microbial community analysis that integrates many third party tools which
- have become standard in the field. A standard QIIME analysis begins with
- sequence data from one or more sequencing platforms, including
-  * Sanger,
-  * Roche/454, and
-  * Illumina GAIIx.
- QIIME can perform:
-  * library de-multiplexing and quality filtering;
-  * denoising with PyroNoise;
-  * OTU and representative set picking with uclust, cdhit, mothur, BLAST,
-    or other tools;
-  * taxonomy assignment with BLAST or the RDP classifier;
-  * sequence alignment with PyNAST, muscle, infernal, or other tools;
-  * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
-  * alpha diversity and rarefaction, including visualization of results,
-    using over 20 metrics including Phylogenetic Diversity, chao1, and
-    observed species;
-  * beta diversity and rarefaction, including visualization of results,
-    using over 25 metrics including weighted and unweighted UniFrac,
-    Euclidean distance, and Bray-Curtis;
-  * summarization and visualization of taxonomic composition of samples
-    using pie charts and histograms
- and many other features.
+ QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
+ package with a focus on data and analysis transparency. QIIME 2 enables
+ researchers to start an analysis with raw DNA sequence data and finish with
+ publication-quality figures and statistical results.
+ Key features:
+  * Integrated and automatic tracking of data provenance
+  * Semantic type system
+  * Plugin system for extending microbiome analysis functionality
+  * Support for multiple types of user interfaces (e.g. API, command line,
+ graphical)
  .
- QIIME includes parallelization capabilities for many of the
- computationally intensive steps. By default, these are configured to
- utilize a mutli-core environment, and are easily configured to run in
- a cluster environment. QIIME is built in Python using the open-source
- PyCogent toolkit. It makes extensive use of unit tests, and is highly
- modular to facilitate custom analyses.
+ QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis
+ pipeline. QIIME 2 will address many of the limitations of QIIME 1, while
+ retaining the features that makes QIIME 1 a powerful and widely-used analysis
+ pipeline.
+ .
+ QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.
+ New functionality will regularly become available through QIIME 2 plugins. You
+ can view a list of plugins that are currently available on the QIIME 2 plugin
+ availability page. The future plugins page lists plugins that are being
+ developed. 



View it on GitLab: https://salsa.debian.org/med-team/qiime/commit/1ae71cf2f21289d4ef3519b994888c256166017a

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View it on GitLab: https://salsa.debian.org/med-team/qiime/commit/1ae71cf2f21289d4ef3519b994888c256166017a
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