安装 interproscan
SFLD errors： https://github.com/ebi-pf-team/interproscan/wiki/KnownIssues
运行报错：
Command: bin/blast/ncbi-blast-2.3.0+/rpsbproc -i /home/pangel/interproscan-5.24-63.0/temp/dellcmb.bnu.edu.cn_20170619_150332200_361c//jobCDD/000000000001_000000000006.blast.raw.out -d data/cdd/3.14/data -m std
Error output from binary:
bin/blast/ncbi-blast-2.3.0+/rpsbproc: symbol lookup error: bin/blast/ncbi-blast-2.3.0+/rpsbproc: undefined symbol: _ZZN4ncbi16CNcbiEmptyString3GetEvE9empty_str
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echo _ZZN4ncbi16CNcbiEmptyString3GetEvE9empty_str|c++filt
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原来是 ncbi::CNcbiEmptyString::Get()::empty_str 没有定义
解决办法：https://github.com/ebi-pf-team/interproscan/wiki/KnownIssues
For CDD/rpsblast errors, copy the files in ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/bin/rh6/rpsblast_binary.zip into bin/blast/ncbi-blast-2.3.0+/
遗憾的是还是报错。
源码编译：
The "rpsblast" binary can be obtained from ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.3.0/ and the "rpsbproc" from ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc
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下载新的ncbi－blast和rpsbproc后还是报错：
bin/blast/ncbi-blast-2.3.0+/rpsbproc: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by bin/blast/ncbi-blast-2.3.0+/rpsbproc)
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只得源码安装了。 源码安装 Source: ncbi－blast＋：ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/README
2. DOWNLOAD AND COMPILE APPLICATIONS FOR YOUR SYSTEM
-------------------------------------------------
The rpsbproc executable, as well as rpsblast and rpstblastn, are NCBI toolbox
applications and therefore require NCBI toolbox to compile. It is recommended
that you download the lastest blast+ package from:
ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/
Retrieve the source code package (xxxxx-src.tar.gz for unix family systems or
xxxxx-src.zip for windows systems) and decompress. This package includes all
necessary toolkit libraries, tools and scripts to build the applications.
At the time of writing, the current version is 2.2.30, so the archive
decompresses into a tree:
ncbi-blast-2.2.30+-src
|-c++
|-compilers...
|-include...
|-scripts...
|-src
|-app
|-...
Next, download rpsbproc-src.zip or rpsbproc-src.tar.gz from:
ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/
Decompress it to ncbi-blast-2.2.30+-src/c++/src/app so that a directory
"rpsbproc" appears under ncbi-blast-2.2.30+-src/c++/src/app, which contains
four files:
ncbi-blast-2.2.30+-src/c++/src/app/rpsbproc/rpsbproc.cpp
ncbi-blast-2.2.30+-src/c++/src/app/rpsbproc/Makefile
ncbi-blast-2.2.30+-src/c++/src/app/rpsbproc/Makefile.in
ncbi-blast-2.2.30+-src/c++/src/app/rpsbproc/Makefile.RpsbProc.app
After adding the source file, edit
ncbi-blast-2.2.30+-src/c++/src/app/Makefile.in and
add "RpsbProc" (case sensitive) to the "SUB_PROJ" line.
Now the toolkit and rpsblast application are ready to be built. Scripts are
already created to build the toolkit on different OS platforms, please refer
to the following document for detailed build instructions for your particular
platform:
http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_config/
If the compilation is successful, binaries should be in
ncbi-blast-2.2.30+-src/c++/<built-type>/bin/ or
ncbi-blast-2.2.30+-src/c++/compilers/<compiler>/static/bin/<built-type>.
Copy the rpsblast, rpstblastn and rpsbproc executables to your local blast
directory, such as ~/localrpsb. The toolkit source codes are no longer needed
and can be deleted.
cd /home/pangel/interproscan-5.24-63.0/bin/blast/ncbi-blast-2.3.0+-src/c++/src/app
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修改MakeFile.in
...
SUB_PROJ = rpsbproc RpsbProc asn2asn asn2fasta asn2flat asnval asn_cleanup \
...
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cd /home/pangel/interproscan-5.24-63.0/bin/blast/ncbi-blast-2.3.0+-src/c++/
./configure --prefix=/path/to/install
cd /home/pangel/interproscan-5.24-63.0/bin/blast/ncbi-blast-2.3.0+-src/c++/ReleaseMT/build && make all_r
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OK!