Andreas Tille pushed to branch master at Debian Med / qiime
Commits: ab34735d by Andreas Tille at 2018-10-28T17:07:53Z Remove more remainings of qiime1 - - - - - 2 changed files: - − debian/qiime.1.ronn - − debian/qiime.dirs Changes: ===================================== debian/qiime.1.ronn deleted ===================================== @@ -1,73 +0,0 @@ -qiime(1) -- Quantitative Insights Into Microbial Ecology - -This is a short manpage for QIIME on Debian/Bio-Linux. -You should refer to the main QIIME documentation at -/usr/share/doc/qiime/html/index.html and also the QIIME section of the -Bio-Linux tutorial at http://environmentalomics.org/bio-linux-training/. - -## INVOCATION: - -To run any QIIME command such as "validate_mapping_file.py": - - _$_ `qiime` validate_mapping_file [...] - -or just type 'qiime' to get a customised shell environment where all QIIME commands -are available exactly as documented, ie: - - _$_ `qiime` - - _$ qiime >_ `validate_mapping_file.py` [...] - -## PARAMETERS FILE: - -For certain QIIME commands, you are asked to indicate where your QIIME -parameters file is. You can find an example file in the location -/usr/share/doc/qiime/qiime_parameters_example.txt but the recommendation -as of QIIME 1.7.0 is to only set values that you want to override and to -let QIIME pick defaults for the others. - -## QIIME CONFIGURATION: - -QIIME reads configuration information from the file specified by -**$QIIME_CONFIG_FP** or by default from **/etc/qiime/qiime_config**. -It is unlikely you will need to change the settings in this file, -but if you do you should copy it as **.qiime_config** in your home directory. - -## GREENGENES DATA: - -The qiime-data package now provides copies of the Greengenes core alignment -template plus the lanemask file in **/usr/share/qiime/data** but you still need -to download some extra data to use QIIME properly. Taxonomic databases are -being updated all the time and you need to be sure which version you are -using. See the QIIME main docs for more info on what you need. - -## PROGRAMS INVOKED BY QIIME: - -QIIME calls many applications and libraries in the course of performing an -analysis. For consistency, it is important to know what versions were installed -at the time of the analysis. To obtain a complete report type - - `print_qiime_config_all` - -**NB:** The official release of QIIME stipulates very particular versions of all these -programs in order to guarantee consistent results. This version of QIIME uses updated -versions that are packages in the Debian software repository. If you want to obtain ressults -consistent with the official QIIME pipeline then you need to install QIIME as set out on -the main website. - -## UCLUST and USEARCH: - -You may install these manually if you want to use them, but as of QIIME 1.9 -all features should be available via the free SumaClust and vSearch programs. -uClust and uSearch are not free software and come with usage restrictions -for non-paying users. - -For more info, try running 'uclust' or 'usearch' at the QIIME prompt. - -## For more information about QIIME, please visit the home page at: - - http://qiime.org - -## QIIME was packaged as part of the Bio-Linux project. - - http://environmentalomics.org/bio-linux ===================================== debian/qiime.dirs deleted ===================================== @@ -1 +0,0 @@ -usr/lib/qiime/bin View it on GitLab: https://salsa.debian.org/med-team/qiime/commit/ab34735db47e5102f44ff8b0809710b77dd67022 -- View it on GitLab: https://salsa.debian.org/med-team/qiime/commit/ab34735db47e5102f44ff8b0809710b77dd67022 You're receiving this email because of your account on salsa.debian.org.
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