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Python 3 is a different language and is currently not supported. Galaxy is distributed and developed using a distributed version control system called Mercurial.


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The AMI already includes mercurial version Remove the existing bedtools package, and install a newer one. Remove the old version, get the new version, unpack and compile it, and then put it where it can be found.

The Galaxy Project

The development and release repositories are available through the bitbucket hosting service. Often you can just fire up Galaxy at this point. However, we want a few things to be different from the default installation. However, if the file already exists it is not copied over. Copy the file and update it:.

Galaxy, like WebApollo and several other components that are also covered at the course, will listen to port by default; to avoid stomping on that earlier work, we will configure Galaxy to listen to a different port. Out of the box Galaxy includes the embedded SQLite database. This allows Galaxy to run with zero-configuration and provides an excellent solution for single-user Galaxy installations being used for tool development.

The Galaxy Project. Presentation

However, for any multi-user scenario a more robust database will be needed for Galaxy to be reliable. We highly recommend Postgres , although other databases are known to work. The ubuntu user has permission to create databases, so let's create the database that we told Galaxy to connect to:. Galaxy includes a script to run it. This script also performs the Galaxy initialization the first time it is run.

Run it now:. Once the database is initialized, the normal startup process proceeds, loading tool configurations, starting the job runner, and finally initializing the web interface on the requested port. Without any additional configuration, there is already a lot we can do with our first Galaxy instance. As an example, let's work through an analysis that is based on, but distinct from the Galaxy tutorial. Registering is not required in order to use Galaxy. However, to use all of it, users need to register.

We scooped up an unknown beast out of the slime and sent it off to the sequencing core to get it sequenced and an assembly so we can study it. Turns out it's an archaea, and it's new. We have subsequently run the assembly through a gene prediction pipeline, and have also identified potential transcription binding sites TFBSs using another pipeline. This brings up the upload data form from which you can. We are going to use the URL option. This will import those 4 datasets your history. Let's take a look at the data. For each dataset,. Join genes with TFBS , with min overlap of 1 bp. Takes the two bed files and joins them together into double-wide records where the first n columns are from the genes dataset and the last columns are from the repeats dataset.

Furthermore, it only creates records when an gene and a TFBS overlap. Now we want to walk through the pairings and count the number of times each gene occurs. This number is the number of TFBS that overlap with each gene.

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We are going to do another operation that is borrowed from relational databases. Select the gene-TFBS pairings dataset and set Group by column to c4 , the column in the dataset that contains the gene name. This tells Galaxy to walk through the dataset, create a group for each different value of column 4 the gene name , and then count the number of records that were in that group i.

This produces a two column dataset. The first column is the value of the column we grouped by. The second is the number of records in the dataset that have that gene name. We have the list of genes, and the counts in them. We could use this dataset in further analysis, email it someone, etc.. However, we can do better. We have lost some information about the genes like position, strand, and so on that we had in the original gene dataset.

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If we can reclaim that information, and add to it, we can produce a more useful dataset that we can visualize right now. The original gene dataset downloaded from UCSC had a meaningless score column. Let's replace that with the repeat count. Set the first dataset to Genes with repeat counts and the second to be the original Genes dataset. Join them using column c1 and column c4 , which are the gene names in both datasets. This produces and a dataset with the gene repeat counts in the first two columns and the gene information in the rightmost columns.

Now, use the Cut tool to reshuffle these columns into a valid 6 column BED file with the repeat count in column 5, the score column.


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He waved his hands, and nothing seemed to happen. Then people gasped and pointed into the sky. A dozen or so black shapes were descending from the sky. Seven of them were similar in size and shape - large rectangular craft with two smaller rectangles off to each side. These made a deep thrumming noise as they approached, and the flags of major Earth nations could be seen imprinted on them.

Behind them were four other craft. One a giant golden pyramidal ship, another a round white ship with a glowing thing not unlike a star inside it, and a smaller blue ship with alien writing all over it. The fourth larger ship seemed to be of a similar design to the seven other craft, but much larger and with four rectangular structures around the center. Are you ready for the delegates? The blue ship - apparently designated the Commeral - drifted to just above the president, and shot out a beam of light and a series of rings appeared on the stage behind him.

Suddenly, there were several delegates standing there, each with their nations flag or symbol imprinted on their shirts: all of which no-one had ever seen before. One delegate caused a collective gasp. She was obviously not human, but some kind of humanoid reptile. Hayes smirked as the people all started talking.

The other world leaders motioned for silence as well, but the crowd was too busy yelling. Got it? By the way, just beamed up the shooter. He seems to not be all there, if you know what I mean. Hayes rolled his eyes. They are from the only nation that currently occupies more than one world, the Hebridan Commerce. Their society is half human, half Serrakin, and they live together in harmony, just like we hope we can.

The Galaxy Project - Chapter 1 - GMBlackjack - Stargate - All Series [Archive of Our Own]

With the additions of these peoples, we now effectively own a somewhat large section of the cosmos. We also have highly advanced technology gifted to us by the dying race known as the Asgard, which ensures our safety as we continue to explore the galaxy. We should be extremely honored to receive the legacy of the Great Alliance that spanned the galaxy millions of years ago. While the UN will be keeping the Asgard technology strictly regulated, we will be giving the less advanced but still world changing technology to the public domain so everyone can make it.


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We expect that within five years we will be able to construct civilian starships, solve the energy crisis, and put a serious dent in world hunger now that we can use all these technologies out in the open. Earth will become the center of a new age in space. You two can come down now.