从零开始学生信-meme的安装和使用 - Yuan-SW-F(abysw)

时间：2024-02-01 13:31:48

从零开始学生信-meme的安装和使用

软件：meme-suit

用途：鉴定motif

目的：其实我这里主要是为了使用streme模块（因为sequence number超过50）。

办法：

1. 如果只安装meme，可以直接用conda install -c bioconda meme。

2. 如果需要所有的套件，需要手动安装：

　　准备好gcc 和 make

　　下载meme

　　安装

整个过程很简单，本章只讲安装，安装实际尝试顺序讲，下一章讲使用。

最后的整个过程会被去掉报错部分，调整为最直接的方案，系统整理到微信公众号：生物信息分析学习 中。

 

 详细步骤如下：

$ wget http://meme-suite.org/meme-software/5.3.0/meme-5.3.0.tar.gz

$ tar zxvf meme-5.3.0.tar.gz

$ ./configure --prefix=/Yuan/app/meme --with-url="http://meme-suite.org"

出现报错：

$ ./configure --prefix=/Yuan/app/meme --with-url="http://meme-suite.org"
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... no
checking whether make supports nested variables... no
checking whether make supports nested variables... (cached) no
checking for gcc... no
checking for cc... no
checking for cl.exe... no
configure: error: in `/Yuan/soft/meme-5.3.0\':
configure: error: no acceptable C compiler found in $PATH
See `config.log\' for more details

原因：全新的集群，没有gcc什么的，需要安装一下。

但是，既然万物皆可conda，看看：

 

 果然有，直接安装：

$ conda install -c bioconda meme

$ which meme
/Yuan/app/anaconda3/bin/meme

安装完成。

那我一定要编译呢？

$ gcc

Command \'gcc\' not found, but can be installed with:

apt install gcc

$ apt install gcc

继续报错：

$ apt install gcc
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-9 gcc-9 gcc-9-base libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0
libcrypt-dev libctf-nobfd0 libctf0 libgcc-9-dev libgomp1 libisl22 libitm1 liblsan0 libmpc3 libquadmath0 libtsan0 libubsan1 linux-libc-dev manpages-dev
Suggested packages:
binutils-doc cpp-doc gcc-9-locales gcc-multilib make autoconf automake libtool flex bison gdb gcc-doc gcc-9-multilib gcc-9-doc glibc-doc
The following NEW packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-9 gcc gcc-9 gcc-9-base libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0
libcrypt-dev libctf-nobfd0 libctf0 libgcc-9-dev libgomp1 libisl22 libitm1 liblsan0 libmpc3 libquadmath0 libtsan0 libubsan1 linux-libc-dev manpages-dev
0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded.
Need to get 28.6 MB of archives.
After this operation, 123 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://in.archive.ubuntu.com/ubuntu focal/main amd64 binutils-common amd64 2.34-6ubuntu1 [207 kB]
Get:2 http://in.archive.ubuntu.com/ubuntu focal/main amd64 libbinutils amd64 2.34-6ubuntu1 [474 kB]
Get:3 http://in.archive.ubuntu.com/ubuntu focal/main amd64 libctf-nobfd0 amd64 2.34-6ubuntu1 [47.0 kB]
Get:4 http://in.archive.ubuntu.com/ubuntu focal/main amd64 libctf0 amd64 2.34-6ubuntu1 [46.6 kB]
Get:5 http://in.archive.ubuntu.com/ubuntu focal/main amd64 binutils-x86-64-linux-gnu amd64 2.34-6ubuntu1 [1,614 kB]
Get:6 http://in.archive.ubuntu.com/ubuntu focal/main amd64 binutils amd64 2.34-6ubuntu1 [3,376 B]
Get:7 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 gcc-9-base amd64 9.3.0-17ubuntu1~20.04 [19.1 kB]
Get:8 http://in.archive.ubuntu.com/ubuntu focal/main amd64 libisl22 amd64 0.22.1-1 [592 kB]
Get:9 http://in.archive.ubuntu.com/ubuntu focal/main amd64 libmpc3 amd64 1.1.0-1 [40.8 kB]
Get:10 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 cpp-9 amd64 9.3.0-17ubuntu1~20.04 [7,494 kB]
Get:11 http://in.archive.ubuntu.com/ubuntu focal/main amd64 cpp amd64 4:9.3.0-1ubuntu2 [27.6 kB]
Get:12 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libcc1-0 amd64 10.2.0-5ubuntu1~20.04 [41.1 kB]
Get:13 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libgomp1 amd64 10.2.0-5ubuntu1~20.04 [102 kB]
Get:14 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libitm1 amd64 10.2.0-5ubuntu1~20.04 [26.4 kB]
Get:15 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libatomic1 amd64 10.2.0-5ubuntu1~20.04 [9,300 B]
Get:16 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libasan5 amd64 9.3.0-17ubuntu1~20.04 [394 kB]
Get:17 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 liblsan0 amd64 10.2.0-5ubuntu1~20.04 [144 kB]
Get:18 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libtsan0 amd64 10.2.0-5ubuntu1~20.04 [320 kB]
Get:19 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libubsan1 amd64 10.2.0-5ubuntu1~20.04 [136 kB]
Get:20 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libquadmath0 amd64 10.2.0-5ubuntu1~20.04 [146 kB]
Get:21 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libgcc-9-dev amd64 9.3.0-17ubuntu1~20.04 [2,360 kB]
Get:22 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 gcc-9 amd64 9.3.0-17ubuntu1~20.04 [8,241 kB]
Get:23 http://in.archive.ubuntu.com/ubuntu focal/main amd64 gcc amd64 4:9.3.0-1ubuntu2 [5,208 B]
Get:24 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libc-dev-bin amd64 2.31-0ubuntu9.1 [71.7 kB]
Ign:25 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 linux-libc-dev amd64 5.4.0-58.64
Get:26 http://in.archive.ubuntu.com/ubuntu focal/main amd64 libcrypt-dev amd64 1:4.4.10-10ubuntu4 [104 kB]
Get:27 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 libc6-dev amd64 2.31-0ubuntu9.1 [2,519 kB]
Get:28 http://in.archive.ubuntu.com/ubuntu focal/main amd64 manpages-dev all 5.05-1 [2,266 kB]
Err:25 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 linux-libc-dev amd64 5.4.0-58.64
404 Not Found [IP: 43.255.166.254 80]
Fetched 27.5 MB in 5s (5,337 kB/s)
E: Failed to fetch http://in.archive.ubuntu.com/ubuntu/pool/main/l/linux/linux-libc-dev_5.4.0-58.64_amd64.deb 404 Not Found [IP: 43.255.166.254 80]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

根据建议，更新：

$ apt-get update

更新之后重新安装gcc

$ apt install gcc

安装成功

$ which gcc
/usr/bin/gcc

重新安装meme

config.status: error: in `/Yuan/soft/meme-5.3.0\':
config.status: error: Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. If GNU make was not used, consider
re-running the configure script with MAKE="gmake" (or whatever is
necessary). You can also try re-running configure with the
\'--disable-dependency-tracking\' option to at least be able to build
the package (albeit without support for automatic dependency tracking).
See `config.log\' for more details

报错：没有make 和 gmake

$ make

Command \'make\' not found, but can be installed with:

apt install make # version 4.2.1-1.2, or
apt install make-guile # version 4.2.1-1.2

 $ apt install make

$ which make
/usr/bin/make

重新编译meme：

========================
Configuration parameters
========================

Install path: /Yuan/app/meme-5.3.0
Install UID:
Version: 5.3.0
C compiler: gcc
C compiler flags: -std=gnu89 -fno-common -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -O3
Linker: /usr/bin/ld -m elf_x86_64
Special Libs: -lm
MPICC gcc
MPIRUN
MPI_CMD
MPIINC
MPILIBDIR
MPIFLAGS
SOURCE URL:
WEBSITE URL: http://meme-suite.org
ALTERNATE WEBSITE URL:
PREVIOUS VERSION URL:
SERVER CONTACT:
DEVELOPER CONTACT: meme-suite@uw.edu
GO-SERVER URL: http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID
XBUILD:
PERL: /Yuan/app/anaconda3/bin/perl
PYTHON: /Yuan/app/anaconda3/bin/python
PYTHON VERSiON: 3.8
CONVERT:
GHOSTSCRIPT: /Yuan/app/anaconda3/bin/gs
BUILD LIBXML2: no
LIBXML2 compiler flags: -I/Yuan/app/anaconda3/include/libxml2 -I/Yuan/app/anaconda3/include
LIBXML2 libs: -L/Yuan/app/anaconda3/lib -lxml2 -L/Yuan/app/anaconda3/lib -lz -L/Yuan/app/anaconda3/lib -llzma -lpthread -L/Yuan/app/anaconda3/lib -L/Yuan/app/anaconda3/lib -licui18n -licuuc -licudata -lm -ldl
BUILD LIBXSLT: no
LIBXSLT compiler flags: -I/Yuan/app/anaconda3/include/libxml2 -I/Yuan/app/anaconda3/include
LIBXSLT libs: -L/Yuan/app/anaconda3/lib -lxslt -lxml2 -lpthread -licui18n -licuuc -licudata -ldl -lm -lrt
MEME DB: ${datarootdir}/${PACKAGE_NAME}-5.3.0/db
MEME LOGS: ${localstatedir}/${PACKAGE_NAME}-5.3.0/LOGS
MEME TEMP FILES:
OPAL URL: no
OPAL DEPLOY DIRECTORY:

Run the following commands to compile, test and install meme:
make
make test
make install

Then make sure that the following two directories are added to
your PATH variable:
/Yuan/app/meme-5.3.0/bin
/Yuan/app/meme-5.3.0/libexec/meme-5.3.0

This can often be done by editing the file named .profile to add
the following line:
export PATH=/Yuan/app/meme-5.3.0/bin:/Yuan/app/meme-5.3.0/libexec/meme-5.3.0:$PATH

无报错，接下一步：

make

make test 

make install

 

 好了，完事。

meme的使用，网上有一大堆例子，也没有什么好说的。