宏基因流程python后台部署

ice-melt

宏基因流程python后台部署

代码仓库地址

git@192.168.0.156:/home/git/python/docker_build.git
git@192.168.0.156:/home/git/python/GS_PY3.git

初始环境部署

# 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

部署过程命令

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

# 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/

# 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

# krona                                                                    
cd $WS/docker_build/krona
conda activate krona
pip uninstall easy_krona
python setup.py sdist
python setup.py install

# metaphlan2                                                               
cd $WS/docker_build/metaphlan
conda activate metaphlan2
pip uninstall easy_mpa
python setup.py sdist
python setup.py install

ice-melt

metaphlan 2.7.7 报错

# 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

修改：

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)
    ...

ice-melt

lefse 1.0.8.post1 报错

# 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

修改：~/miniconda2/envs/lefse/bin/lefse-plot_cladogram.py

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 > np.pi else False
	while totseps > 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'] )