跟着官网安装说明做即可,注意装好conda后最好更换一下conda和pip源，不然网速会让你抓狂的
via http://qiime.org/install/install.html
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| System information
==================
Platform: linux2
Python version: 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:09:15) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
Python executable: /home/ferstar/anaconda3/envs/qiime/bin/python
QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3
Dependency versions
===================
QIIME library version: 1.9.1
QIIME script version: 1.9.1
qiime-default-reference version: 0.1.3
NumPy version: 1.10.4
SciPy version: 0.17.1
pandas version: 0.18.1
matplotlib version: 1.4.3
biom-format version: 2.1.5
h5py version: Not installed. # 这个不能装
qcli version: 0.1.1
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.51
burrito version: 0.9.1
burrito-fillings version: 0.1.1
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.00
swarm version: Swarm 1.2.19 [Apr 12 2017 17:30:22]
gdata: Installed.
QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html
http://qiime.org/tutorials/parallel_qiime.html
blastmat_dir: None
pick_otus_reference_seqs_fp: /home/ferstar/anaconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue: all.q
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: /home/ferstar/anaconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
cluster_jobs_fp: start_parallel_jobs.py
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: /home/ferstar/anaconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue: friendlyq
jobs_to_start: 1
slurm_time: None
denoiser_min_per_core: 50
assign_taxonomy_id_to_taxonomy_fp: /home/ferstar/anaconda3/envs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: blastall
seconds_to_sleep: 1
QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.022s
OK
|
关于ssh终端如何使用matplotlib画图的问题
via http://stackoverflow.com/questions/2801882/generating-a-png-with-matplotlib-when-display-is-undefined
方法有很多, 由于我是管理员, 所以选择一个全局的方案, 如下:
>>> import matplotlib
>>> matplotlib.matplotlib_fname()
u'/prodata/miniconda2/envs/qiime/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc'
打开这个文件, 把backend改成agg即可, 首字母a不区分大小写
更换清华大学conda源
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| $ vi ~/.condarc
channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
- bioconda
- r
- defaults
- conda-forge
show_channel_urls: true
|
更换阿里pip源
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| $ mkdir ~/.pip
$ vi ~/.pip/pip.conf
[global]
trusted-host = mirrors.aliyun.com
index-url = http://mirrors.aliyun.com/pypi/simple
|