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Alex Buchanan buchanae

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buchanae / saga.py
Created August 15, 2018 22:28
hello
@buchanae
buchanae / gist:28ddb05419a0826dc15bec4bd39cb223
Created August 4, 2018 00:43
pip install pyarrow
Collecting pyarrow
Downloading https://files.pythonhosted.org/packages/be/2d/11751c477e4e7f4bb07ac7584aafabe0d0608c170e4bff67246d695ebdbe/pyarrow-0.9.0.tar.gz (8.5MB)
100% |████████████████████████████████| 8.5MB 5.2MB/s
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-kbc7nj85/pyarrow/setup.py", line 29, in <module>
from Cython.Distutils import build_ext as _build_ext
ModuleNotFoundError: No module named 'Cython'
@buchanae
buchanae / example.md
Created July 19, 2018 16:23 
import mygene
mg = mygene.MyGeneInfo()
mg.querymany("BRCA1", returnall=True)
querying 1-1...done.

Finished.

@buchanae
buchanae / sge.yml
Created May 23, 2018 22:50
Compute: gridengine
GridEngine:
Template: |
#!/bin/bash
#$ -N {{.TaskId}}
#$ -o {{.WorkDir}}/funnel-stdout
#$ -e {{.WorkDir}}/funnel-stderr
{{if ne .Cpus 0 -}}
{{printf "#$ -pe mpi %d" .Cpus}}
@buchanae
buchanae / optimize.go
Last active February 21, 2018 17:57
package main
import (
"fmt"
"sort"
"github.com/bmeg/arachne/aql"
"github.com/ohsu-comp-bio/mortar/graph"
"github.com/ohsu-comp-bio/tes"
)
@buchanae
buchanae / status.go
Created December 25, 2017 19:27
package main
import (
"context"
"strings"
"encoding/json"
"bufio"
"fmt"
//"github.com/ohsu-comp-bio/funnel/server/boltdb"
//"github.com/ohsu-comp-bio/funnel/config"
@buchanae
buchanae / example-ladon.go
Created December 7, 2017 23:07
package main
import (
"fmt"
"github.com/ory/ladon"
manager "github.com/ory/ladon/manager/memory"
)
func main() {
@buchanae
buchanae / file_task.go
Created September 29, 2017 02:09
type FileTaskReader struct {
Path string
task *tes.Task
}
func (f *FileTaskReader) Task() (*tes.Task, error) {
if f.task != nil {
return f.task, nil
}
@buchanae
buchanae / bolt_locking.go
Last active May 31, 2017 02:33
Trying to understand locking in BoltDB
package main
import "io/ioutil"
import "fmt"
import "github.com/boltdb/bolt"
import "sync"
import "time"
func update(id string, val string) func(*bolt.Tx) error {
@buchanae
buchanae / abs-files.wdl
Last active November 1, 2016 21:12
workflow AbsoluteOutputFiles {
call MakeFilesTask
}
task MakeFilesTask {
command {
mkdir -p /mnt/datastore/resultdata
date > /mnt/datastore/resultdata/output
}