Here are the tools we use to help you
Custom software development
We use Play/Activate web framework with Scala for web front ends along with Ruby on Rails and some other options. Back end processing scripts are written in Perl or shell scripts, mostly.
We use google drive for shared long term design files. Current status and to do lists are in Asana. Tactical discussion can occur in Slack or google hangouts. Customer access to all these tools is not only possible, but strongly encouraged.
We like to use git and Gitlab for distributed version control. Jenkins handles workflow automation and automated unit testing. Zabbix is a great tool for monitoring server operation and graphing trends. Ansible automates configuration. The industry standard ELK stack is ideal for logging. SLURM is our preferred queuing and batch processing system.