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。