Christophe Faucon pfaucon
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| ... | |
| Wrappers for the new NCBI BLAST+ tools (written in C++): | |
| - NcbiblastpCommandline - Protein-Protein BLAST | |
| - NcbideltablastCommandline - Protein-Protein domain enhanced lookup time accelerated blast | |
| ... | |
pfaucon
/ Applications_with_delta_blast.py
Created
December 28, 2013 16:33
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| # Copyright 2001 Brad Chapman. | |
| # Revisions copyright 2009-2010 by Peter Cock. | |
| # Revisions copyright 2010 by Phillip Garland. | |
| # All rights reserved. | |
| # This code is part of the Biopython distribution and governed by its | |
| # license. Please see the LICENSE file that should have been included | |
| # as part of this package. | |
| """Definitions for interacting with BLAST related applications. | |
| Obsolete wrappers for the old/classic NCBI BLAST tools (written in C): |
pfaucon
/ stratos_dev_buildscript_output
Created
April 8, 2014 22:38
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| ----------------- short version ---------------- | |
| vagrant@paas:~$ ./stratos_dev.sh -b | |
| export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64/ | |
| Running 'mvn clean install'. | |
| ~ ~ | |
| Listening for transport dt_socket at address: 8888 | |
| [INFO] Scanning for projects... | |
| [ERROR] The build could not read 1 project -> [Help 1] | |
| [ERROR] |
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| ==> default: Importing base box 'mortar-precise64-1400765389'... | |
| ==> default: Matching MAC address for NAT networking... | |
| ==> default: Setting the name of the VM: mortar_sandbox | |
| ==> default: Fixed port collision for 22 => 2222. Now on port 2200. | |
| ==> default: Clearing any previously set network interfaces... | |
| ==> default: Preparing network interfaces based on configuration... | |
| default: Adapter 1: nat | |
| ==> default: Forwarding ports... | |
| default: 22 => 2200 (adapter 1) | |
| ==> default: Running 'pre-boot' VM customizations... |
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| christophes-pro:bcbio pfaucon$ sh vagrant_osx.sh | |
| --2014-10-02 15:45:03-- https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/vm/Vagrantfile | |
| Resolving raw.github.com... 23.235.47.133 | |
| Connecting to raw.github.com|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 301 Moved Permanently | |
| Location: https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/vm/Vagrantfile [following] | |
| --2014-10-02 15:45:04-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/vm/Vagrantfile | |
| Resolving raw.githubusercontent.com... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK |
pfaucon
/ gist:6057cbcab7ebab5f96f7
Created
October 9, 2014 16:16
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| [Restored contents truncated] | |
| Selecting previously unselected package libxpp3-java. | |
| Preparing to unpack .../libxpp3-java_1.1.4c-2build1_all.deb ... | |
| Unpacking libxpp3-java (1.1.4c-2build1) ... | |
| Selecting previously unselected package libdom4j-java. | |
| Preparing to unpack .../libdom4j-java_1.6.1+dfsg.3-2ubuntu1_all.deb ... | |
| Unpacking libdom4j-java (1.6.1+dfsg.3-2ubuntu1) ... | |
| Selecting previously unselected package libosgi-core-java. | |
| Preparing to unpack .../libosgi-core-java_4.3.0-4_all.deb ... | |
| Unpacking libosgi-core-java (4.3.0-4) ... |
pfaucon
/ gist:6f7c2ba0328ce38cb22b
Last active
August 29, 2015 14:08
minimum obj-c to reproduce textview issue
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| -(void)awakeFromNib | |
| { | |
| if(!self.descriptionTextView) | |
| { | |
| self.descriptionTextView = [[UITextView alloc] initWithFrame:self.bounds]; | |
| self.descriptionTextView.text = @"Lorem ipsum dolor sit er elit lamet, consectetaur cillium adipisicing pecu, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. Nam liber te conscient to factor tum poen legum odioque civiuda.Lorem ipsum dolor sit er elit lamet, consectetaur cillium adipisicing pecu, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit |
pfaucon
/ gist:67bab93ce44b754348ea
Created
November 4, 2014 16:52
Gist from the latest run - SRR950078 only
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| vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ bcbio_nextgen.py ../config/seqc.yaml -n 8 | |
| [2014-10-30 16:28] Using input YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-30 16:28] Checking sample YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml | |
| [2014-10-30 16:28] Testing minimum versions of installed programs | |
| [2014-10-30 16:28] Resource requests: AlienTrimmer, picard; memory: 2.0, 3.5; cores: 1, 1 | |
| [2014-10-30 16:28] Configuring 1 jobs to run, using 1 cores each with 3.8g of memory reserved for each job | |
| [2014-10-30 16:28] Timing: adapter trimming | |
| [2014-10-30 16:28] multiprocessing: prepare_sample | |
| [2014-10-30 16:28] Preparing UHRR_rep1 | |
| [2014-10-30 16:28] multiprocessing: trim_sample |
pfaucon
/ gist:a8195ca4286ae905e6aa
Created
May 27, 2015 07:03
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| Loaded assembly: /Users/User/Library/Developer/CoreSimulator/Devices/7BDF52FF-E614-40B4-9453-B01D806DEB00/data/Containers/Bundle/Application/12B1602F-49BB-453E-BAA7-7982DE9FE793/WebServicesRxNormSample.app/monotouch.dll [External] | |
| Loaded assembly: /Users/User/Library/Developer/CoreSimulator/Devices/7BDF52FF-E614-40B4-9453-B01D806DEB00/data/Containers/Bundle/Application/12B1602F-49BB-453E-BAA7-7982DE9FE793/WebServicesRxNormSample.app/System.Core.dll [External] | |
| Loaded assembly: /Users/User/Library/Developer/CoreSimulator/Devices/7BDF52FF-E614-40B4-9453-B01D806DEB00/data/Containers/Bundle/Application/12B1602F-49BB-453E-BAA7-7982DE9FE793/WebServicesRxNormSample.app/System.dll [External] | |
| Loaded assembly: /Users/User/Library/Developer/CoreSimulator/Devices/7BDF52FF-E614-40B4-9453-B01D806DEB00/data/Containers/Bundle/Application/12B1602F-49BB-453E-BAA7-7982DE9FE793/WebServicesRxNormSample.app/WebServicesRxNormSample.exe | |
| Loaded assembly: /Users/User/Library/Developer/CoreSimulator/Devices/7BDF52FF-E614-40B4-9453-B01D8 |
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| Process: WebServicesRxNormSample [44805] | |
| Path: /Users/USER/Library/Developer/CoreSimulator/Devices/7EB4CBDC-0E69-4D72-A098-1CFA195CC6CD/data/Containers/Bundle/Application/684D803A-B9B1-4A6D-985A-E907A5AA261E/WebServicesRxNormSample.app/WebServicesRxNormSample | |
| Identifier: WebServicesRxNormSample | |
| Version: 1.0 | |
| Code Type: X86 (Native) | |
| Parent Process: launchd_sim [44741] | |
| Responsible: launchd_sim [44741] | |
| User ID: 501 | |
| Date/Time: 2015-05-27 08:54:25.828 +0200 |
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