$$==========================================================$$ $$ $$ $$ Task description for CCP4 Package Manager $$ $$ LINUX VERSION $$ $$ $$ $$==========================================================$$ $$ "version" referes to the version of Package Manager. $$ $$ Package Manager will refuse improper versions and $$ $$ prompt the user to update $$ 1.00 $$ "fetch" records specify data that Package Manager $$ $$ downloads from CCP4 server and keeps internally. Data $$ $$ type is idntified by the "type" attribute, which must $$ $$ have one of predefined values. $$ unpack.py install_core.py seticon.py ccp4i.png coot.png ccp4mg.png list.txt conditions.txt arpwarp_license.txt coot_license.txt ccp4mg_license.txt {b}Collaborative Computational Project No. 4{/b}{br} {font size="-1"} Science and Technology Facilities Council{br} Rutherford Appleton Laboratory{br} Didcot, Oxon, OX11 0FA, United Kingdom{br} http://www.ccp4.ac.uk{br} {/font} {br} {h1}CCP4 Software Suite{/h1} {h3}Version 6.3{/h3} {h2}Setup{/h2} {br} This program will guide you through the setup process and{br} install CCP4 Software Suite on your computer. {p} Press "Next" button to continue. 1 1 $$ Choice/suggestion for operationg system (OS) $$ $$ List of supported operating systems $$ RedHat 4 64-bit CentOS 4 32-bit CentOS 5 32-bit CentOS 5 64-bit RedHat 5 32-bit Fedora 10 32-bit Fedora 12 32-bit Fedora 14 32-bit Ubuntu 8.04 32-bit Ubuntu 10.04 32-bit Ubuntu 10.04 64-bit openSUSE 11.3 64-bit $$ Explanation notes to be displayed on the page $$ Most of CCP4 Software Suite components are independent of a particular Linux flavour. If your Operating System is not found in the provided list, choose OS that matches your system most closely, either by name or by RedHat/Debian origin. Note that 64-bit distributions will not work on 32-bit systems. If your system is 64-bit, you need to install 32-bit run-time libraries regardless of the choice.{p} If your system is not in the list {b}and{/b} your installation was not successful, {b}please{/b} let us know a) your system's name and release (such as "Ubuntu 11.04 32 bit") b) what was your choice of system for the installation. This will allow us to improve CCP4 distribution by increasing system coverage. Thank you for your assistance. 1 1 $$ Server from which components will be downloaded $$ http://www.ccp4.ac.uk/setup/linux $$ "item" describes an installed component. "select" may $$ $$ be "yes" (initially selected), "no" (initially $$ $$ inselected) or "must" (always selected). $$ $$ Name to appear in the list of components $$ CCP4 Program Suite v6.3.0 core $$ "size" shows approximate unpacked size in KBs $$ 1200000 $$ "erase" gives sub-directory name to erase for clean $$ $$ installation. This record is not mandatory, and as $$ $$ many of them, as necessary, may be given. $$ $$ DO NOT give the same "erase" record in more than $$ $$ one component! $$ ccp4-6.3.0 $$ "subdir" gives sub-directory name, where the $$ $$ corresponding tarball will be unpacked. This record $$ $$ is mandatory and must be synchronised with the actual $$ $$ content of tarballs. $$ ccp4-6.3.0 $$ Description to appear next to the list of components $$ CCP4 core packages. Collection of over 200 usefull programs, written by various authors, which provides tools for all stages of structure solution process, plus software libraries and accompanying data. Core packages are needed for other applications in the list. $$ File name pattern to download. All files with names $$ $$ starting with the pattern will be downloaded if the $$ $$ item is selected. This may be conditional to other $$ $$ selections, if "ref" tag is provided. $$ core1. core1-64. $$ If "ref" attribute is given for a pattern, that $$ $$ pattern will be used if all referenced components $$ $$ ("ref" may have any number of comma-separated $$ $$ references) are selected for installation. $$ core2. core2-64. $$ The installer will check if a file specified in $$ $$ "check_dependency" is visible under PATH $$ {check_dependency}tclsh{/check_dependency} $$ If "icon" record is given and the corresponding, as $$ $$ identified by otem's reference, icon has been $$ $$ fetched, the installer will put the icon on the $$ $$ desktop with name given by "name" atribute and $$ $$ executable with path given in the statement, appended $$ $$ to the destination directory + subdir. This job is $$ $$ done by "icon_script.py". $$ ccp4i.sh $$ There may be as many items as necessary $$ ARP/wARP v7.3 arpwarp 205000 arp_warp_7.3 arp_warp_7.3 ARP/wARP is Crystallographic Macromolecular Building Software from EMBL-Hamburg.{p} Note that this software is not covered by CCP4 licence. Members of not publically funded academic and/or education and/or research institutions must obtain a commercial ARP/wARP license from {a href="http://www.arp-warp.org"} http://www.arp-warp.org{/a} prior selecting Arp/wArp for download. $$ "phony=yes" indicates that the component is included $$ $$ into another component's package(s), where a proper $$ $$ pattern is chosen conditoionally through the "ref" $$ $$ attribute. The package specified by phony pattern $$ $$ is never attempted for download and may not exist, $$ $$ however, some name should be provided. $$ core-arpwarp. {name_pattern}arpwarp.{/name_pattern} $$ "check_component" forces selection of the referenced $$ $$ if "this" component is selected $$ core COOT v0.6.2 coot 350000 coot-0.6.2 coot-0.6.2 Coot, the Crystallographic Object-Oriented Toolkit. An interactive graphical application for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more. {p} Note that Coot is platform-dependent and may not work in some Linux systems. $$ "os" attribute specifies an operating system. "os" $$ $$ must be one of those listed in "os" page. If "os" is $$ $$ omitted, the package is consedered to be available $$ $$ for any platform, however this will be overwritten if $$ $$ a matching platform is found in "os" attribute of $$ $$ another package. $$ coot-0.6.2-centos-4. coot-0.6.2-rhel-4-64. coot-0.6.2-centos-4. coot-0.6.2-rhel-4-64. coot-0.6.2-rhel-5. coot-0.6.2-centos-5-64. coot-0.6.2-rhel-5. coot-0.6.2-centos-5-64. coot-0.6.2-fedora-10. coot-0.6.2-fedora-10. coot-0.6.2-fedora-12. coot-0.6.2-fedora-12. coot-0.6.2-fedora-14. coot-0.6.2-ubuntu-8.04. coot-0.6.2-ubuntu-8.04. coot-0.6.2-ubuntu-10.04. coot-0.6.2-ubuntu-10.04-64. coot-0.6.2-opensuse-11.3-64. $$ Packages for all other platforms $$ coot-0.6.2-rhel-5. coot-0.6.2-centos-5-64. coot-0.6.2-rhel-5. coot-0.6.2-centos-5-64. coot-0.6.2-fedora-14. coot-0.6.2-centos-5-64. coot-0.6.2-ubuntu-10.04. coot-0.6.2-ubuntu-10.04-64. coot-0.6.2-ubuntu-10.04. coot-0.6.2-ubuntu-10.04-64. coot-0.6.2-opensuse-11.3-64. coot-0.6.2-rhel-5. coot-0.6.2-centos-5-64. bin/coot Balbes Database balbes_db 3000000 ccp4-6.3.0 Database of models for Automatic Macromolecular Replacement pipeline BALBES (part of CCP4 Program Suite). Contains a comprehensive set of models taken from PDB archive, manually curated and prepared for use with BALBES. This archive is needed only if you are going to use BALBES software. balbes_db. $$ "check_component" forces selection of the referenced $$ $$ if "this" component is selected $$ core CCP4mg v2.6.0 ccp4mg 920000 ccp4mg-2.6.0 ccp4mg-2.6.0 CCP4mg (Molecular Graphics) is the quick and easy way to create beautiful publication quality images and movies. It is also the easy way to superpose and analyse structures. CCP4mg provides for a range of model drawing styles include ribbons, surfaces, spheres, ball-and-stick and surfaces. CCP4mg also displays electron density as cylinders or 2D slices. The viewer may be used for movie making, automatic protein superposition (using SSM software) and protein assembly analysis (based on PISA software). {p} Note that CCP4mg is platform-dependent and may not work in some Linux systems. $$ Packages for specific platforms $$ mg-older-64. mg-centos-4. mg-centos-4. mg-older-64. $$ Package for all other platforms $$ mg-modern. mg-modern-64. bin/ccp4mg Chooch v5.0.2 chooch 16500 ccp4-6.3.0 CHOOCH is a program that will automatically determine values of the anomalous scattering factors, f' and f'', directly from experimentally measured X-ray fluorescence data. It outputs the f' and f'' spectrum and the appropriate X-ray wavelengths to be used for MAD or SAD experiments. chooch.tar.gz 1 1 1 $$ absence of "ref" tag indicates unconditional licence, $$ $$ which will be always requested to agree with $$ 1 1 1 $$ There may be as many licence pages as necessary. $$ $$ There may be as many reference records as necessary, $$ $$ however, only first reference will be used to identify $$ $$ appropriate licence text from fetch records. $$ arpwarp $$ Request category indicates that licence approval $$ $$ should be sought from external server. The server will $$ $$ respond with word "Approved" if licence is granted, $$ $$ and give a reason for refusal (if any) otherwise. $$ $$ url gives server's url, must end with question mark $$ http://www.embl-hamburg.de/arp-cgi-bin/ccp4download? $$http://www.ccp4.ac.uk/setup/linux/approve.txt?$$ $$ Each item will be displayed for user's input with $$ $$ prompts as given by the record. User's input is $$ $$ communicated to the server in tuples "id=value", $$ $$ where "id" is given in item's attributes. Values are $$ $$ sent percentage-encoded. $$ First name: Surname: E-mail: $$ "type" is a special id, which makes combobox with $$ $$ two values: "academic" and "commercial". User's $$ $$ selection is communicated to server as $$ $$ "licence=academic" or "licence=commercial". $$ $$ Optional "key" attribute specifies whether a field $$ $$ for licence key should be displayed. If key="yes" $$ $$ then licence key is send to server as key=value. $$ Licence type: 1 1 1 $$ There may be as many reference records as necessary, $$ $$ however, only first reference will be used to identify $$ $$ appropriate licence text from fetch records. $$ coot 1 1 1 ccp4mg 1 1 1 Choose directory where CCP4 Software should be installed: Choose temporary directory for download: $$ modify_global_env: $$ absent or 0: do not modify $$ 1: show prompt with default yes $$ 2: show prompt with default no 2 1 1 1 1 1 1 unpack.py install.py 1 1