弄完我才知道為何很多人吐槽這個(gè)軟件的Linux版本很難用，各種報(bào)錯(cuò)都是淚呀辅鲸。大概正確的安裝和運(yùn)行操作如下格郁，很多教程遇到的坑我就不寫(xiě)了。
首先去maxquant的官網(wǎng)去獲得maxquant這個(gè)軟件，點(diǎn)擊下載你就要提交一個(gè)申請(qǐng)例书，它會(huì)自動(dòng)發(fā)到你郵箱锣尉，然后就可以下載
image.png
然后把這個(gè)軟件分別在window上面一份以及在Linux上面一份
安裝環(huán)境
如果奇怪我為何用的是mamba而不是conda可以看這個(gè) mamba極速安裝conda包
mamba create -n Promaxquant
conda activate Promaxquant
mamba install -y -c conda-forge https://anaconda.org/conda-forge/dotnet/3.1.409/download/linux-64/dotnet-3.1.409-ha770c72_0.tar.bz2
## 需要3.1.1 左右的.net
mamba install -y -c conda-forge maxquant
###其實(shí)這個(gè)maxquant沒(méi)有意義，需要的是其中附帶的mono
然后使用windows版本生成相應(yīng)的mqpar.xml 文件决采，然后最好是手動(dòng)修改mqpar.xml的路徑（雖然它有推薦有相應(yīng)的命令,在這個(gè)youtube視頻以及官網(wǎng)上都可以找到）自沧，如何用windows版本生成可以參考這個(gè)視頻
MQSS 2021 | Pre-course: How to run MaxQuant on Linux | Pavel Sinitcyn - YouTube
確認(rèn)好mqpar.xml的文件路徑正確之后，激活相應(yīng)的conda環(huán)境树瞭，然后可以運(yùn)行拇厢，需要的是MaxQuantCmd.exe（注意有Cmd這個(gè)）
(Promaxquant) [lp@localhost data]$ mono MaxQuant_v2.2.0.0/bin/MaxQuantCmd.exe TestRAW/mqpar.xml
Configuring
Assemble run info
Finish run info
Testing fasta files
Testing raw files
Feature detection
Deisotoping
MS/MS preparation
Calculating peak properties
Combining apl files for first search
Preparing searches
MS/MS first search
Read search results for recalibration
Mass recalibration
Calculating masses
MS/MS preparation for main search
Combining apl files for main search
MS/MS main search
Preparing combined folder
Correcting errors
Reading search engine results
Preparing reverse hits
Finish search engine results
Filter identifications (MS/MS)
Calculating PEP
Copying identifications
Applying FDR
Assembling second peptide MS/MS
Combining second peptide files
Second peptide search
Reading search engine results (SP)
Finish search engine results (SP)
Filtering identifications (SP)
Applying FDR (SP)
Re-quantification
Reporter quantification
Prepare protein assembly
Assembling proteins
Assembling unidentified peptides
Finish protein assembly
Updating identifications
Estimating complexity
Prepare writing tables
Writing tables
Finish writing tables
下面這些命令我不知道有沒(méi)有用，因?yàn)槲乙彩前擦松古纾恢烙袥](méi)有解決其中的依賴(lài)孝偎，理論上應(yīng)該不用運(yùn)行和安裝下面的命令
# For CentOS 7:
yum install centos-release-scl
yum install devtoolset-8
scl enable devtoolset-8 -- bash
# Enable the tools (put this into .bash_profile)
source /opt/rh/devtoolset-8/enable
還有一些命令可以參考tc3/maxquant_linux_guide
