mjhjmtu

I got ncbi-blast: not found despite it should be there (https://packages.debian.org/jessie/amd64/ncbi-blast+/download)

FROM debian:jessie
# based on https://github.com/docker-library/php/blob/master/5.6/jessie/apache/Dockerfile

RUN apt-get update && apt-get install -y --no-install-recommends 
 libapache2-mod-perl2 
 libcgi-pm-perl 
 php5-cgi 
 php5-mysql 
 libapache2-mod-php5 
 php5-mysql 
 php5-gd && 
 ncbi-blast+ && 
 rm -rf /var/lib/apt/lists/*

What did I miss?

As Mark Plotnick commented, it appears you rearranged the lines at some point, adding the line for ncbi-blast+ after pgp5-gd, but you forgot to remove the && at the end of php5-gd so that the next continuation line lists another package instead of ending the previous command. The command as you had it would have requested installation of the packages up until php5-gd, after which it would have tried to execute ncbi-blast+, which presumably wasn't already installed, and so would have thrown an error, after which it would not have run the rm command. Use the following, instead:

RUN apt-get update && apt-get install -y --no-install-recommends 
 libapache2-mod-perl2 
 libcgi-pm-perl 
 php5-cgi 
 php5-mysql 
 libapache2-mod-php5 
 php5-mysql 
 php5-gd 
 ncbi-blast+ && 
 rm -rf /var/lib/apt/lists/*