<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[宏基因流程python后台部署]]></title><description><![CDATA[<h1>宏基因流程python后台部署</h1>
<h2>代码仓库地址</h2>
<ul>
<li><a href="mailto:git@192.168.0.156" rel="nofollow ugc">git@192.168.0.156</a>:/home/git/python/docker_build.git</li>
<li><a href="mailto:git@192.168.0.156" rel="nofollow ugc">git@192.168.0.156</a>:/home/git/python/GS_PY3.git</li>
</ul>
<h2>初始环境部署</h2>
<pre><code class="language-sh"># 安装conda（略）
# 创建相应的环境 -c bioconda                                                
conda create -n lefse -y lefse=1.0.8.post1
conda create -n metaphlan2 -y metaphlan2=2.7.7
conda create -n krona -y krona=2.7.1
conda create -n GS_PY3 -y python=3.8 r=4.0.3

</code></pre>
<h2>部署过程命令</h2>
<pre><code class="language-sh">export WS="/home/bioinfo/workspace"
export CONDA="/home/bioinfo/miniconda2"

# 1.clone代码                                                              
cd $WS
git clone git@192.168.0.156:/home/git/python/docker_build.git
git clone git@192.168.0.156:/home/git/python/GS_PY3.git
</code></pre>
<pre><code class="language-sh"># 2.安装GS_PY3                                                             
cd $WS/GS_PY3
conda activate GS_PY3
pip uninstall GS_PY3
python setup.py sdist
python setup.py install
cp ./bin/gs_py3_fq_stat $CONDA/envs/GS_PY3/bin/
</code></pre>
<pre><code class="language-sh"># 3.安装 docker_build 相关软件扩展                                           
# lefse
cd $WS/docker_build/lefse
conda activate lefse
pip uninstall easy_lefse
python setup.py sdist
python setup.py install
</code></pre>
<pre><code class="language-sh"># krona                                                                    
cd $WS/docker_build/krona
conda activate krona
pip uninstall easy_krona
python setup.py sdist
python setup.py install
</code></pre>
<pre><code class="language-sh"># metaphlan2                                                               
cd $WS/docker_build/metaphlan
conda activate metaphlan2
pip uninstall easy_mpa
python setup.py sdist
python setup.py install

</code></pre>
]]></description><link>http://an.forum.genostack.com/topic/141/宏基因流程python后台部署</link><generator>RSS for Node</generator><lastBuildDate>Sat, 13 Jun 2026 12:31:35 GMT</lastBuildDate><atom:link href="http://an.forum.genostack.com/topic/141.rss" rel="self" type="application/rss+xml"/><pubDate>Fri, 18 Dec 2020 07:29:34 GMT</pubDate><ttl>60</ttl><item><title><![CDATA[Reply to 宏基因流程python后台部署 on Tue, 22 Dec 2020 06:16:36 GMT]]></title><description><![CDATA[<h1>lefse 1.0.8.post1 报错</h1>
<pre><code class="language-sh"># 170 
lefse-plot_cladogram.py  all_add_groups.res all_add_groups_cladogram.png --format png --clade_sep 0.05 --abrv_stop_lev 7 --dpi 500
# 报错: AttributeError: Unknown property axis_bgcolor
</code></pre>
<p dir="auto">修改：~/miniconda2/envs/lefse/bin/lefse-plot_cladogram.py</p>
<pre><code>def draw_tree(out_file,tree,params):
	plt_size = 7
	nlev = tree['nlev']
	pt_scale = (params['min_point_size'],max(1.0,((tree['max_abs']-tree['min_abs']))/(params['max_point_size']-params['min_point_size'])))
	depth = len(nlev)
	sep = (2.0*np.pi)/float(nlev[-1]) 
	seps = [params['clade_sep']*sep/float(depth-i+1) for i in range(1,len(tree['nlev'])+1)]
	totseps = sum([s*nlev[i] for i,s in enumerate(seps[:-1])])
	clade_sep_err = True if totseps &gt; np.pi else False
	while totseps &gt; np.pi:
		params['clade_sep'] *= 0.75 	 
		seps = [params['clade_sep']*sep/(float(depth-i+1)*0.25) for i in range(1,len(tree['nlev'])+1)]
		totseps = sum([s*nlev[i] for i,s in enumerate(seps[:-1])])
	if clade_sep_err: print 'clade_sep parameter too large, lowered to',params['clade_sep']

	fig = plt.figure(edgecolor=params['back_color'],facecolor=params['back_color'])
	ax = fig.add_subplot(111, polar=True, frame_on=False,facecolor=params['back_color'] )
	# axis_bgcolor 修改为 facecolor
	#ax = fig.add_subplot(111, polar=True, frame_on=False, axis_bgcolor=params['back_color'] )
</code></pre>
]]></description><link>http://an.forum.genostack.com/post/255</link><guid isPermaLink="true">http://an.forum.genostack.com/post/255</guid><dc:creator><![CDATA[ice-melt]]></dc:creator><pubDate>Tue, 22 Dec 2020 06:16:36 GMT</pubDate></item><item><title><![CDATA[Reply to 宏基因流程python后台部署 on Fri, 18 Dec 2020 08:37:46 GMT]]></title><description><![CDATA[<h1>metaphlan 2.7.7 报错</h1>
<pre><code class="language-sh"># 170
metaphlan_hclust_heatmap.py --in /home/bioinfo/software/cromwell/cromwell-executions/demo_2020_12_15_20_22_35_copy/60edd0a5-84ba-4328-bee7-2df493f29ae3/call-easyMpa_8/inputs/273451736/mpa_merge_table.txt --out hm_a.png --tax_lev a -c bbcry -s log --top 25 --in /home/bioinfo/software/cromwell/cromwell-executions/demo_2020_12_15_20_22_35_copy/60edd0a5-84ba-4328-bee7-2df493f29ae3/call-easyMpa_8/inputs/273451736/mpa_merge_table.txt --minv 0.1

# 报错 ： AttributeError: Unknown property axisbg
</code></pre>
<p dir="auto">修改：</p>
<pre><code class="language-python">def heatmap_panel( fig, D, minv, maxv, idx1, idx2, cm_name, scale, cols, rows, label_font_size, cb_offset, cb_l, flabelson, slabelson, cm_ticks, gridon, bar_offset ):
    cm = pylab.get_cmap(cm_name)
    bottom_col = [    cm._segmentdata['red'][0][1],
                      cm._segmentdata['green'][0][1],
                      cm._segmentdata['blue'][0][1]   ]
    axmatrix = fig.add_axes( [0.0,0.0,1.0,1.0]) # 去除axisbg
    # axmatrix = fig.add_axes( [0.0,0.0,1.0,1.0], axisbg=bottom_col)
    ...
</code></pre>
]]></description><link>http://an.forum.genostack.com/post/248</link><guid isPermaLink="true">http://an.forum.genostack.com/post/248</guid><dc:creator><![CDATA[ice-melt]]></dc:creator><pubDate>Fri, 18 Dec 2020 08:37:46 GMT</pubDate></item></channel></rss>