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bioinformatics.Rmd
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bioinformatics.Rmd
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# 生物信息 {#bioinfo}
## 微生物组 {#microbiome}
##### 1. Ubuntu 20.04 安装 qiime1 {-}
直接按文档中所说 `conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock
nose -c bioconda` 出现错误 PackagesNotFoundError matplotlib=1.4.3
解决办法是创建新的 conda 环境 `qiime1`, `conda create -n qiime1 python=2.7`, 然后用 pip 手动安装 matplotlib 及其他的 python 模块
```
# 1 安装matplotlib==1.4.3的时候，出现错误 "The following required packages can
# not be built: * freetype", pip 不能安装系统依赖，手动安装系统依赖后然后安装
sudo apt-get install libfreetype6-dev libxft-dev
pip install matplotlib==1.4.3
# 2 qiime中要求biom-format>=2.1.4,<2.2.0,但是目前版本不支持python 2.7
# 手动安装2.1.4版本
pip install biom-format==2.1.4
# 3 最后安装qiime
pip install qiime
# 检测安装是否成功
print_qiime_config.py -t
```
pick otu 或者 嵌合体识别 (chimera) 可用 usearch61 方法, 安装 usearch步骤为
[下载](https://drive5.com/downloads/usearch6.1.544_i86linux32.gz)解压后,
拷贝到 `/usr/local/bin/` 然后赋予执行权限:
```sh
sudo mv usearch* /usr/local/bin/usearch61
# 添加权限
chmod a+x /usr/local/bin/usearch61
```
##### 2. ubuntu 20.04 安装 picrust1 {-}
按照文档中说的`conda create -n picrust1 -c bioconda -c conda-forge picrust`
安装出现错误 `failed with repodata from current_repodata.json`。
只使用 `bioconda`可正常安装, `conda create -n picrust1 -c bioconda picrust`.
##### 3. mac安装 lefse {-}
通过homebrew安装lefse已经[不再维护](https://github.com/biobakery/homebrew-biobakery/issues/37)`brew install biobakery/biobakery/lefse`;采用conda安装(目前biobakery下的软件都用[conda源安装](https://bitbucket.org/biobakery/biobakery/wiki/biobakery_advanced#rst-header-installing-individual-biobakery-tools))
```sh
conda config --add channels biobakery
conda install -c biobakery lefse
```
##### 4. Q: 本地测试qiime1脚本时，安装完依赖后，运行脚本，pycharm 导入 matplotlib.pyplot 出现错误 `from urllib.parse import urlencode ImportError: No module named parse` {-}
pycharm中设置 `Preferences -> Tools -> Python Scientific`取消勾选`Show plots in tool window`，答案见[此](https://stackoverflow.com/questions/57267016/pycharm-import-matplotlib-pyplot-show-error)
##### 5. Q: phyloseq 中 `distance()` 或 `ordinate()` (调用 `distance()`) 基于树计算距离的时候(如 `unifrac`), 出现 `Warning message: In matrix(tree$edge[order(tree$edge[, 1]), ][, 2], byrow = TRUE, : data length [86515] is not a sub-multiple or multiple of the number of rows [43258]`
原因是因为对 OTU 进行质控的时候 (如删除丰度较低的 OTU)，原因是
树不是二分树，解决办法是转化为二分树。参考[这里](https://github.com/joey711/phyloseq/issues/936#issuecomment-569000555)
```r
new_tre <- ape::multi2di(phy_tree(ps))
phy_tree(ps) <- new_tre
```
## scRNA-seq
- 安装[velocyto.R](https://github.com/velocyto-team/velocyto.R).
- `clang: error: unsupported option '-fopenmp'`
mac下clang不支持openmp，解决方法参考[此处](https://github.com/BUStools/BUSpaRse)，安装支持openmp的[clang](https://cran.r-project.org/bin/macosx/tools/). 然后修改配置文件，在`~/.R/Makevars`(配置compliers和library)，添加
```
CC=/usr/local/clang7/bin/clang
SHLIB_CXXLD=/usr/local/clang7/bin/clang++
CXX= /usr/local/clang7/bin/clang++ -Wall
CXX1X= /usr/local/clang7/bin/clang++
CXX98= /usr/local/clang7/bin/clang++
CXX11= /usr/local/clang7/bin/clang++
CXX14= /usr/local/clang7/bin/clang++
CXX17= /usr/local/clang7/bin/clang++
LDFLAGS=-L/usr/local/clang7/lib
```
- `library not found for -lboost_filesystem`
安装 boost `brew install boost`
- `library not found for -lgfortran`
gfortran包含在gcc中，但是电脑中gcc是通过homebrew安装，原始配置文件`/Library/Frameworks/R.framework/Resources/etc/Makeconf`中并没有更新库的地址，在`~/.R/Makevars`中手动添加即可
```
# 通过homebrew安装的gcc地址
FLIBS = -L/usr/local/lib/gcc/8/gcc/x86_64-apple-darwin17.5.0/8.1.0 -L/usr/local/lib/gcc/8 -lgfortran -lquadmath -lm
# Library/Frameworks/R.framework/Resources/etc/Makeconf中的原始配置
# FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
```
- 安装[`velocyto.py`](https://github.com/velocyto-team/velocyto.py)
mac 在 pip 安装的时候gcc编译出现错误，建议使用conda安装`conda install velocyto.py`
## RNA structure
本节记录在 RNA 结构生物信息学分析中的一些问题，如 RNA 二级结构预测。
### 软件安装
#### 二级结构预测 {-}
- [CONTRAfold](http://contra.stanford.edu/contrafold/download.html), 按照帮助
手册`make`的时候出现错误
```
LBFGS.ipp:110:33: error: ‘DoLineSearch’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
Real step = DoLineSearch(x[k%2], f[k%2], g[k%2], d,
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
x[(k+1)%2], f[(k+1)%2], g[(k+1)%2],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Real(0), std::min(Real(10), MAX_STEP_NORM / std::max(Real(1), Norm(d))));
```
解决办法(见[这里](https://github.com/zavolanlab/snoRNAHybridSearchPipeline/blob/master/doics/installation.rst))：
1. Makefile中添加 `-fpermissive` 选项至 `CSXXFLAGS`:
```
CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall -fpermissive
# 替换
CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall
```
2. `Utilities.hpp`中添加`#include <limits.h>`