Thanks for the answer! Right now I'm only considering Pipeline Pilot as an alternative, but would you mind elaborating on how data importation is easier in iPlant? I haven't really thought of Galaxy's data importation as lacking, but I'm open to hearing about what I'm missing.
Pipeline Pilot Vs. Galaxy For Nextgen Data Analysis
I have used Pipeline Pilot in the past for cheminformatics work, and I found it to be a great system for data analysis and reporting.
In my current job I've been using Galaxy extensively, and I have a pretty good idea of its strengths and peccadilloes. It's a lot like Pipeline Pilot, which leads to my question: has anyone here used both Pipeline Pilot and Galaxy for NextGen data analysis? I've read through the marketing material from Accelrys, but I haven't talked to anyone yet who has used Pipeline Pilot's nextgen package for their data crunching.
Specifically, I'd like to know if there is anything in the NextGen world that Pipeline Pilot can do that would make it a worthwhile paid alternative to Galaxy, which is free.
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You can take a look at iPlant's discovery environment (http://www.iplantcollaborative.org), it has tools to do RNA-seq data analysis ( and a lot more). Its greatest strengths are that it is a lot easier to load data into it than galaxy and you can request the tools of your choosing to be added in a reasonable (1 week at most) amount of time.
I haven't really used galaxy much myself, but i know it is way easier to upload data files of any size, through a set of command line tools into iplant and the management of the data is almost as easy as you already do it into your desktop computer, iplant has lots of space, so much that we are going to host galaxy itself in a near future. you can get more info at: https://pods.iplantcollaborative.org/wiki/display/start/Storing+Your+Data+with+iPlant+and+Accessing+that+Data
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i had worked on pipeline pilot for the NGS collection. its a wonderful collection as compared to any other softwares, even galaxy. the advantages are: 1. uploading the input files using an offline software is quite easier rather than waiting in a queue using an online software like galaxy 2. the protocol or the software for our analysis is designed by us and not by someone. This helps one to customize our protocol 3. for every single experiment, one has to do lots of intermediate steps in galaxy, but in this, the complex steps are encapsulated as a component and our work is just to drag that component and put it appropriately.
Pipeline pilot not only helps to execute a job, but also teaches OOP concept. its a complete software toolbox and acts like a software lego for building a software