changeset 1:d734579c3307 draft

Uploaded
author bgruening
date Tue, 24 Feb 2015 08:55:29 -0500
parents db68266f7364
children 38b08a771e7e
files readme.md readme.rst
diffstat 2 files changed, 83 insertions(+), 84 deletions(-) [+]
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line diff
--- a/readme.md	Tue Feb 24 04:48:44 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-Galaxy workflow for the identification of candidate genes clusters
-------------------------------------------------------------------
-
-This approach screens two proteins against all nucleotide sequence from the
-NCBI nt database within hours on our cluster, leading to all organisms with an inter-
-esting gene structure for further investigation. As usual in Galaxy workflows every
-parameter, including the proximity distance, can be changed and additional steps
-can be easily added. For example additional filtering to refine the initial BLAST
-hits, or inclusion of a third query sequence.
-
-![Workflow Image](https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/find_genes_located_nearby.png)
-
-
-Sample Data
-===========
-
-As an example, we will use two protein sequences from *Streptomyces aurantiacus*
-that are part of a gene cluster, responsible for metabolite producion.
-
-You can upload both sequences directly into Galaxy using the "Upload File" tool
-with either of these URLs - Galaxy should recognise this is FASTA files.
-
- * https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658548.fasta
- * https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658557.fasta
-
-In addition you can find both sequences at the NCBI server:
- * http://www.ncbi.nlm.nih.gov/protein/739806622 (cytochrome P450)
- 
-```text
->gi|739806622|ref|WP_037658557.1| cytochrome P450 [Streptomyces aurantiacus]
-MQRTCPFSVPPVYTKFREESPITQVVLPDGGKAWLVTKYDDVRAVMANPKLSSDRRAPDFPVVVPGQNAA
-LAKHAPFMIILDGAEHAAARRPVISEFSVRRVAAMKPRIQEIVDGFIDDMLKMPKPVDLNQVFSLPVPSL
-VVSEILGMPYEGHEYFMELAEILLRRTTDEQGRIAVSVELRKYMDKLVEEKIENPGDDLLSRQIELQRQQ
-GGIDRPQLASLCLLVLLAGHETTANMINLGVFSMLTKPELLAEIKADPSKTPKAVDELLRFYTIPDFGAH
-RLALDDVEIGGVLIRKGEAVIASTFAANRDPAVFDDPEELDFGRDARHHVAFGYGPHQCLGQNLGRLELQ
-VVFDTLFRRLPELRLAVPEEELSFKSDALVYGLYELPVTW
-```
-
- * http://www.ncbi.nlm.nih.gov/protein/739806613 (beta-ACP synthase)
-
-```
->gi|739806613|ref|WP_037658548.1| beta-ACP synthase [Streptomyces aurantiacus]
-MSGRRVVVTGMEVLAPGGVGTDNFWSLLSEGRTATRGITFFDPAQFRSRVAAEIDFDPYAHGLTPQEVRR
-MDRAAQFAVVAARGAVADSGLDTDTLDPYRIGVTIGSAVGATMSLDEDYRVVSDAGRLDLVDHTYADPFF
-YNYFVPSSFATEVARLVGAQGPSSVVSAGCTSGLDSVGYAVELIREGTADVMVAGATDAPISPITMACFD
-AIKATTPRHDDPEHASRPFDDTRNGFVLGEGTAVFVLEELESARRRGARIYAEIAGYATRSNAYHMTGLR
-PDGAEMAEAITVALDEARMNPTAIDYINAHGSGTKQNDRHETAAFKRSLGEHAYRTPVSSIKSMVGHSLG
-AIGSIEIAASILAIQHDVVPPTANLHTPDPQCDLDYVPLNAREQIVDAVLTVGSGFGGFQSAMVLAQPER
-NAA
-```
-
-
-Citation
-========
-
-If you use this workflow directly, or a derivative of it, or the associated
-NCBI BLAST wrappers for Galaxy, in work leading to a scientific publication,
-please cite:
-
-Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo
-NCBI BLAST+ integrated into Galaxy
-
-http://biorxiv.org/content/early/2015/01/21/014043
-http://dx.doi.org/10.1101/014043
-
-
-Availability
-============
-
-This workflow is available on the main Galaxy Tool Shed:
-
-http://toolshed.g2.bx.psu.edu/view/bgruening/find_genes_located_nearby_workflow
-
-Development is being done on github:
-
-https://github.com/bgruening/galaxytools/workflows/ncbi_blast_plus/
-
-
-Dependencies
-============
-
-These dependencies should be resolved automatically via the Galaxy Tool Shed:
-
-* http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue Feb 24 08:55:29 2015 -0500
@@ -0,0 +1,83 @@
+Galaxy workflow for the identification of candidate genes clusters
+------------------------------------------------------------------
+
+This approach screens two proteins against all nucleotide sequence from the
+NCBI nt database within hours on our cluster, leading to all organisms with an inter-
+esting gene structure for further investigation. As usual in Galaxy workflows every
+parameter, including the proximity distance, can be changed and additional steps
+can be easily added. For example additional filtering to refine the initial BLAST
+hits, or inclusion of a third query sequence.
+
+.. image:: https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/find_genes_located_nearby.png
+
+
+Sample Data
+===========
+
+As an example, we will use two protein sequences from *Streptomyces aurantiacus*
+that are part of a gene cluster, responsible for metabolite producion.
+
+You can upload both sequences directly into Galaxy using the "Upload File" tool
+with either of these URLs - Galaxy should recognise this is FASTA files.
+
+* `WP_037658548.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658548.fasta>`_
+* `WP_037658557.fasta <https://raw.githubusercontent.com/bgruening/galaxytools/master/workflows/ncbi_blast_plus/find_genes_located_nearby/WP_037658557.fasta>`_
+
+In addition you can find both sequences at the NCBI server:
+ * http://www.ncbi.nlm.nih.gov/protein/739806622 (cytochrome P450)
+   ::
+   
+     >gi|739806622|ref|WP_037658557.1| cytochrome P450 [Streptomyces aurantiacus]
+     MQRTCPFSVPPVYTKFREESPITQVVLPDGGKAWLVTKYDDVRAVMANPKLSSDRRAPDFPVVVPGQNAA
+     LAKHAPFMIILDGAEHAAARRPVISEFSVRRVAAMKPRIQEIVDGFIDDMLKMPKPVDLNQVFSLPVPSL
+     VVSEILGMPYEGHEYFMELAEILLRRTTDEQGRIAVSVELRKYMDKLVEEKIENPGDDLLSRQIELQRQQ
+     GGIDRPQLASLCLLVLLAGHETTANMINLGVFSMLTKPELLAEIKADPSKTPKAVDELLRFYTIPDFGAH
+     RLALDDVEIGGVLIRKGEAVIASTFAANRDPAVFDDPEELDFGRDARHHVAFGYGPHQCLGQNLGRLELQ
+     VVFDTLFRRLPELRLAVPEEELSFKSDALVYGLYELPVTW
+
+
+ * http://www.ncbi.nlm.nih.gov/protein/739806613 (beta-ACP synthase)
+   ::
+  
+     >gi|739806613|ref|WP_037658548.1| beta-ACP synthase [Streptomyces aurantiacus]
+     MSGRRVVVTGMEVLAPGGVGTDNFWSLLSEGRTATRGITFFDPAQFRSRVAAEIDFDPYAHGLTPQEVRR
+     MDRAAQFAVVAARGAVADSGLDTDTLDPYRIGVTIGSAVGATMSLDEDYRVVSDAGRLDLVDHTYADPFF
+     YNYFVPSSFATEVARLVGAQGPSSVVSAGCTSGLDSVGYAVELIREGTADVMVAGATDAPISPITMACFD
+     AIKATTPRHDDPEHASRPFDDTRNGFVLGEGTAVFVLEELESARRRGARIYAEIAGYATRSNAYHMTGLR
+     PDGAEMAEAITVALDEARMNPTAIDYINAHGSGTKQNDRHETAAFKRSLGEHAYRTPVSSIKSMVGHSLG
+     AIGSIEIAASILAIQHDVVPPTANLHTPDPQCDLDYVPLNAREQIVDAVLTVGSGFGGFQSAMVLAQPER
+     NAA
+
+
+Citation
+========
+
+If you use this workflow directly, or a derivative of it, or the associated
+NCBI BLAST wrappers for Galaxy, in work leading to a scientific publication,
+please cite:
+
+Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo
+NCBI BLAST+ integrated into Galaxy
+
+* http://biorxiv.org/content/early/2015/01/21/014043
+* http://dx.doi.org/10.1101/014043
+
+
+Availability
+============
+
+This workflow is available on the main Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/bgruening/find_genes_located_nearby_workflow
+
+Development is being done on github:
+
+https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_genes_located_nearby
+
+
+Dependencies
+============
+
+These dependencies should be resolved automatically via the Galaxy Tool Shed:
+
+* http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus